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  1. Article ; Online: Pathogenesis of Testicular Germ Cell Neoplasia: A Conceptual Approach.

    Baraban, Ezra G / Cooper, Kumarasen

    Advances in anatomic pathology

    2019  Volume 26, Issue 4, Page(s) 241–245

    Abstract: Testicular germ cell tumors are a diverse group of neoplasms, consisting of the prepubertal type 1 tumors, pure teratoma, and pure yolk sac tumor, the type 2 tumors, which are biologically malignant, preceded by germ cell neoplasia in situ, and harbor ... ...

    Abstract Testicular germ cell tumors are a diverse group of neoplasms, consisting of the prepubertal type 1 tumors, pure teratoma, and pure yolk sac tumor, the type 2 tumors, which are biologically malignant, preceded by germ cell neoplasia in situ, and harbor chromosome 12p abnormalities, and the type 3 tumor, spermatocytic tumor, which features chromosome 9p amplification. These arise in distinct clinical settings, and harbor distinct genetic abnormalities, immunohistochemical properties, and morphologic features. Here we have attempted to unify embryology, morphology, immunohistochemistry, and genetics in order to distill this fascinating group of neoplasms into what we hope is a useful framework for understanding their classification.
    MeSH term(s) Biomarkers, Tumor/genetics ; Chromosome Aberrations ; Endodermal Sinus Tumor/pathology ; Germ Cells/pathology ; Humans ; Neoplasms, Germ Cell and Embryonal/diagnosis ; Neoplasms, Germ Cell and Embryonal/genetics ; Neoplasms, Germ Cell and Embryonal/pathology ; Testicular Neoplasms/diagnosis ; Testicular Neoplasms/genetics ; Testicular Neoplasms/pathology
    Chemical Substances Biomarkers, Tumor
    Language English
    Publishing date 2019-04-04
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1212493-x
    ISSN 1533-4031 ; 1072-4109
    ISSN (online) 1533-4031
    ISSN 1072-4109
    DOI 10.1097/PAP.0000000000000233
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  2. Article ; Online: MED15::TFE3

    Argani, Pedram / Matoso, Andres / Baraban, Ezra G / Epstein, Jonathan I / Antonescu, Cristina R

    International journal of surgical pathology

    2023  Volume 31, Issue 4, Page(s) 409–414

    Abstract: We report two novel cases of Xp11 translocation renal cell carcinomas with ... ...

    Abstract We report two novel cases of Xp11 translocation renal cell carcinomas with the
    MeSH term(s) Adult ; Female ; Humans ; Carcinoma, Renal Cell/diagnosis ; Carcinoma, Renal Cell/genetics ; Carcinoma, Renal Cell/pathology ; Translocation, Genetic ; Kidney Neoplasms/diagnosis ; Kidney Neoplasms/genetics ; Kidney Neoplasms/pathology ; Cysts ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics ; Chromosomes, Human, X ; Mediator Complex/genetics
    Chemical Substances ST 679 (104076-16-6) ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; TFE3 protein, human ; MED15 protein, human ; Mediator Complex
    Language English
    Publishing date 2023-01-02
    Publishing country United States
    Document type Review ; Case Reports ; Journal Article
    ZDB-ID 1336393-1
    ISSN 1940-2465 ; 1066-8969
    ISSN (online) 1940-2465
    ISSN 1066-8969
    DOI 10.1177/10668969221143455
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    Zs.A 4500: Show issues Location:
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  3. Article ; Online: Vascular Expression of Prostate-specific Membrane Antigen (PSMA) in MiTF Family Translocation Renal Cell Carcinoma and Related Neoplasms.

    Baraban, Ezra G / Ged, Yasser / Singla, Nirmish / Allaf, Mohammad E / Gorin, Michael A / Markowski, Mark C / Rowe, Steven P / Argani, Pedram

    Applied immunohistochemistry & molecular morphology : AIMM

    2023  Volume 31, Issue 8, Page(s) 544–549

    Abstract: Multiple studies have demonstrated prostate-specific membrane antigen (PSMA) expression in the neo-vasculature of non-prostate tumors including clear cell renal cell carcinoma (ccRCC). However, PSMA expression in rare renal tumors including MiTF family ... ...

    Abstract Multiple studies have demonstrated prostate-specific membrane antigen (PSMA) expression in the neo-vasculature of non-prostate tumors including clear cell renal cell carcinoma (ccRCC). However, PSMA expression in rare renal tumors including MiTF family translocation renal cell carcinoma has not been previously characterized. We examined PSMA expression by immunohistochemistry in a series of MiTF family translocation renal cell carcinomas as well as in several genetically related tumors including alveolar soft part sarcoma and PEComas with TFE3 rearrangements. PSMA expression was also studied in several cases of ccRCC and papillary RCC. Overall, PSMA immunohistochemistry was performed in 61 samples from 58 patients. Vascular PSMA expression was seen with the highest frequency in ccRCC [88% (14/16)] (38% focal, 50% diffuse). Translocation RCC (tRCC) demonstrated the second highest frequency of PSMA expression [71% (22/28)] (57% focal, 14% diffuse), followed by alveolar soft part sarcoma [50% (4/8)] (38% focal, 12% diffuse). No PSMA expression was seen in PEComas with TFE3 rearrangement (0/3) or papillary RCC (0/6). PSMA expression was only present in tumor-associated neo-vasculature. A patient with oligometastatic tRCC underwent 68 Ga-PSMA-11 PET imaging which detected multiple putative metastatic lesions not detected on conventional computed tomography imaging performed 2 weeks prior, supporting the potential utility of PSMA imaging in tRCC. These findings have potential implications for the utility of PSMA guided diagnostic and therapeutic agents in both common and uncommon renal cell carcinoma subtypes as well as genetically related mesenchymal neoplasms.
    MeSH term(s) Humans ; Carcinoma, Renal Cell/diagnosis ; Carcinoma, Renal Cell/genetics ; Carcinoma, Renal Cell/metabolism ; Sarcoma, Alveolar Soft Part ; Kidney Neoplasms/metabolism ; Translocation, Genetic ; Immunohistochemistry
    Language English
    Publishing date 2023-07-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1473273-7
    ISSN 1533-4058 ; 1062-3345 ; 1541-2016
    ISSN (online) 1533-4058
    ISSN 1062-3345 ; 1541-2016
    DOI 10.1097/PAI.0000000000001142
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 3783: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  4. Article ; Online: High-Grade, Nonsarcomatoid Chromophobe Renal Cell Carcinoma: A Series of 22 Cases With Novel Molecular Features on a Subset.

    Baraban, Ezra G / Elias, Roy / Lin, Ming-Tseh / Ged, Yasser / Zhu, Jing / Pallavajjala, Aparna / Singla, Nirmish / Lotan, Tamara L / Argani, Pedram / Eshleman, James R / Epstein, Jonathan I

    Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc

    2024  Volume 37, Issue 5, Page(s) 100472

    Abstract: Chromophobe renal cell carcinoma (ChRCC) is the third most common subtype of renal cell carcinoma and typically exhibits indolent behavior, though a rare subset can exhibit high-grade morphologic features and is associated with a poor prognosis. Although ...

    Abstract Chromophobe renal cell carcinoma (ChRCC) is the third most common subtype of renal cell carcinoma and typically exhibits indolent behavior, though a rare subset can exhibit high-grade morphologic features and is associated with a poor prognosis. Although there are limited data on the molecular characteristics of metastatic and sarcomatoid ChRCC, the molecular features of high-grade, nonsarcomatoid ChRCC remain unexplored. Herein, we characterize 22 cases of ChRCC with high-grade, nonsarcomatoid components. High-grade ChRCC frequently demonstrated advanced stage at diagnosis (64% ≥pT3a or N1), with regions of extrarenal extension, nodal metastases, and vascular invasion consisting solely of high-grade ChRCC morphologically. We performed spatially guided panel-based DNA sequencing on 11 cases comparing high-grade and low-grade regions (n = 22 samples). We identified recurring somatic alterations emblematic of ChRCC, including deletions of chromosomes 1, 2, 6, 10, 13, 17, and 21 in 91% (10/11) of cases and recurring mutations in TP53 (81.8%, n = 9/11) and PTEN (36.4%, n = 4/11). Notably, although PTEN and TP53 alterations were found in both high-grade and low-grade regions, private mutations were identified in 3 cases, indicating convergent evolution. Finally, we identified recurring RB1 mutations in 27% (n = 3) of high-grade regions leading to selective protein loss by immunohistochemistry not observed in adjacent low-grade regions. This finding was confirmed in The Cancer Genome Atlas cohort where 2 of 66 cases contained RB1 mutations and demonstrated unequivocal high-grade, nonsarcomatoid morphology. We also detected multiple chromosomal gains confined to the high-grade regions, consistent with imbalanced chromosome duplication. These findings broaden our understanding of the molecular pathogenesis of ChRCC and suggest that subclonal RB1 mutations can drive the evolution to high-grade, nonsarcomatoid ChRCC.
    MeSH term(s) Humans ; Carcinoma, Renal Cell/genetics ; Carcinoma, Renal Cell/pathology ; Kidney Neoplasms/genetics ; Kidney Neoplasms/pathology ; Middle Aged ; Female ; Male ; Aged ; Adult ; Neoplasm Grading ; Mutation ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/analysis ; Aged, 80 and over
    Language English
    Publishing date 2024-03-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 645073-8
    ISSN 1530-0285 ; 0893-3952
    ISSN (online) 1530-0285
    ISSN 0893-3952
    DOI 10.1016/j.modpat.2024.100472
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    Zs.A 2450: Show issues Location:
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  5. Article ; Online: The "Far Left" of the Morphologic Spectrum of Ovarian High-grade Serous Carcinoma: Case Report of a Purely Noninvasive High-grade Serous Carcinoma Mimicking an Ovarian Serous Borderline Tumor.

    Katsakhyan, Levon / Baraban, Ezra G / Dumoff, Kimberly L / Burger, Robert A / Parikh, Rupal / Cooper, Kumarasen

    International journal of gynecological pathology : official journal of the International Society of Gynecological Pathologists

    2020  Volume 40, Issue 2, Page(s) 175–179

    Abstract: High-grade serous carcinoma has a variety of different growth patterns, but is typically easily recognizable to pathologists and rarely confused with serous borderline tumors. We report a case of a 71-yr-old woman with a unilateral 5.1 cm ovarian cyst ... ...

    Abstract High-grade serous carcinoma has a variety of different growth patterns, but is typically easily recognizable to pathologists and rarely confused with serous borderline tumors. We report a case of a 71-yr-old woman with a unilateral 5.1 cm ovarian cyst with small papillary projections on contrast-enhanced magnetic resonance imaging of the pelvis. Histologic examination showed a noninvasive papillary neoplasm with hierarchical branching and epithelial proliferation, and thus, at low magnification, bearing a striking resemblance to a serous borderline tumor. However, a more careful examination demonstrated high-grade cytologic features, nuclear pleomorphism, and abundant mitotic activity, suggestive of high-grade serous carcinoma. The morphology and immunohistochemical profile of this lesion is consistent with a rare, purely noninvasive growth pattern of high-grade serous carcinoma. This lesion represents the "far left" of the high-grade ovarian serous carcinoma morphologic spectrum and can mimic a serous borderline tumor.
    MeSH term(s) Aged ; Cystadenocarcinoma, Serous/diagnostic imaging ; Cystadenocarcinoma, Serous/pathology ; Female ; Humans ; Hysterectomy ; Immunohistochemistry ; Magnetic Resonance Imaging ; Neoplasms, Glandular and Epithelial/diagnostic imaging ; Neoplasms, Glandular and Epithelial/pathology ; Neoplasms, Glandular and Epithelial/surgery ; Ovarian Cysts/diagnostic imaging ; Ovarian Cysts/pathology ; Ovarian Neoplasms/diagnostic imaging ; Ovarian Neoplasms/pathology ; Ovarian Neoplasms/surgery
    Language English
    Publishing date 2020-03-13
    Publishing country United States
    Document type Case Reports ; Journal Article
    ZDB-ID 604859-6
    ISSN 1538-7151 ; 0277-1691
    ISSN (online) 1538-7151
    ISSN 0277-1691
    DOI 10.1097/PGP.0000000000000668
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    Zs.A 1814: Show issues Location:
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  6. Article: Falsely Increased Plasma Lactate Dehydrogenase without Hemolysis Following Transport through Pneumatic Tube System.

    Herman, Daniel S / Toro, Esmeralda / Baraban, Ezra G / Bagg, Adam / Wang, Ping

    The journal of applied laboratory medicine

    2019  Volume 4, Issue 3, Page(s) 433–438

    Abstract: Background: Lactate dehydrogenase (LDH) is a nonspecific biomarker for diseases including lymphoma. Serum and plasma are generally considered interchangeable for LDH testing. Investigation into falsely increased plasma LDH concentration results led to ... ...

    Abstract Background: Lactate dehydrogenase (LDH) is a nonspecific biomarker for diseases including lymphoma. Serum and plasma are generally considered interchangeable for LDH testing. Investigation into falsely increased plasma LDH concentration results led to the hypothesis that a workflow change that included pneumatic tube system (PTS) transportation caused the errors. The following study was conducted to test the hypothesis.
    Methods: Plasma and serum separator tube samples were each drawn in duplicate, centrifuged, transported either through the PTS or by hand courier, and evaluated by means of clinical chemistry and hematology assays. Smear slides were made out of the plasma and examined. Aggregate patient results before and after the PTS workflow change were compared.
    Results: In post-PTS plasma samples, LDH activity was 26%-149% higher. Similarly, white blood cells (WBCs) were 14- to 156-fold higher and platelets were 1- to 13-fold higher. Smear examination revealed dramatically more cells and cell fragments. No significant hemolysis was observed in plasma by chemistry hemolysis indices or hemoglobin testing. These effects were not observed in similarly transported serum samples in gel separator tubes. Aggregate LDH patient results, including moving medians, demonstrated dramatic changes following PTS workflow implementation.
    Conclusions: PTS transportation led to falsely increased LDH concentration in plasma. These LDH concentration elevations are not heralded by standard indicators of hemolysis. These errors can be prevented by restricting LDH concentration testing to serum collected in gel separator tubes. Moving patient statistics can effectively detect important testing process changes not revealed by external QC or indices.
    MeSH term(s) Blood Chemical Analysis/methods ; Blood Chemical Analysis/standards ; Blood Physiological Phenomena ; Blood Specimen Collection/methods ; Blood Specimen Collection/standards ; Hemolysis ; Humans ; L-Lactate Dehydrogenase/blood ; Specimen Handling/methods ; Specimen Handling/standards ; Transportation
    Chemical Substances L-Lactate Dehydrogenase (EC 1.1.1.27)
    Language English
    Publishing date 2019-08-13
    Publishing country England
    Document type Journal Article
    ISSN 2576-9456
    ISSN 2576-9456
    DOI 10.1373/jalm.2018.028928
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  7. Article: Xyolide, a bioactive nonenolide from an Amazonian endophytic fungus, Xylaria feejeensis

    Baraban, Ezra G / Morin, Jesse B / Phillips, Gillian M / Phillips, Andrew J / Strobel, Scott A / Handelsman, Jo

    Tetrahedron letters. 2013 July 31, v. 54, no. 31

    2013  

    Abstract: Endophytes isolated from tropical plants represent a largely untapped reservoir of bioactive secondary metabolites. We screened a library of fungal endophyte extracts for inhibition of the plant pathogen, Pythium ultimum, and purified an active compound ... ...

    Abstract Endophytes isolated from tropical plants represent a largely untapped reservoir of bioactive secondary metabolites. We screened a library of fungal endophyte extracts for inhibition of the plant pathogen, Pythium ultimum, and purified an active compound using bioassay-guided fractionation. A new nonenolide, (4S,7S,8S,9R)-4-O-succinyl-7,8-dihydroxy-9-heptyl-nonen-9-olide, was isolated and named xyolide. The structure was elucidated by a combination of 1D and 2D NMR methods and the absolute configuration was determined by exciton-coupled circular dichroism. The MIC of xyolide against P. ultimum was 425μM.
    Keywords Pythium ultimum ; Xylaria ; bioactive properties ; chemical reactions ; chemical structure ; endophytes ; fractionation ; fungi ; nuclear magnetic resonance spectroscopy ; organic compounds ; plant pathogens ; secondary metabolites
    Language English
    Dates of publication 2013-0731
    Size p. 4058-4060.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 204287-3
    ISSN 1873-3581 ; 0040-4039
    ISSN (online) 1873-3581
    ISSN 0040-4039
    DOI 10.1016/j.tetlet.2013.05.093
    Database NAL-Catalogue (AGRICOLA)

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    Zs.A 2837: Show issues Location:
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  8. Article: Xyolide, a bioactive nonenolide from an Amazonian endophytic fungus,

    Baraban, Ezra G / Morin, Jesse B / Phillips, Gillian M / Phillips, Andrew J / Strobel, Scott A / Handelsman, Jo

    Tetrahedron letters

    2013  Volume 54, Issue 31, Page(s) 4058–4060

    Abstract: Endophytes isolated from tropical plants represent a largely untapped reservoir of bioactive secondary metabolites. We screened a library of fungal endophyte extracts for inhibition of the plant pathogen, ...

    Abstract Endophytes isolated from tropical plants represent a largely untapped reservoir of bioactive secondary metabolites. We screened a library of fungal endophyte extracts for inhibition of the plant pathogen,
    Language English
    Publishing date 2013-07-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 204287-3
    ISSN 1873-3581 ; 0040-4039
    ISSN (online) 1873-3581
    ISSN 0040-4039
    DOI 10.1016/j.tetlet.2013.05.093
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  9. Article: Genomic and Secondary Metabolite Analyses of Streptomyces sp. 2AW Provide Insight into the Evolution of the Cycloheximide Pathway.

    Stulberg, Elizabeth R / Lozano, Gabriel L / Morin, Jesse B / Park, Hyunjun / Baraban, Ezra G / Mlot, Christine / Heffelfinger, Christopher / Phillips, Gillian M / Rush, Jason S / Phillips, Andrew J / Broderick, Nichole A / Thomas, Michael G / Stabb, Eric V / Handelsman, Jo

    Frontiers in microbiology

    2016  Volume 7, Page(s) 573

    Abstract: The dearth of new antibiotics in the face of widespread antimicrobial resistance makes developing innovative strategies for discovering new antibiotics critical for the future management of infectious disease. Understanding the genetics and evolution of ... ...

    Abstract The dearth of new antibiotics in the face of widespread antimicrobial resistance makes developing innovative strategies for discovering new antibiotics critical for the future management of infectious disease. Understanding the genetics and evolution of antibiotic producers will help guide the discovery and bioengineering of novel antibiotics. We discovered an isolate in Alaskan boreal forest soil that had broad antimicrobial activity. We elucidated the corresponding antimicrobial natural products and sequenced the genome of this isolate, designated Streptomyces sp. 2AW. This strain illustrates the chemical virtuosity typical of the Streptomyces genus, producing cycloheximide as well as two other biosynthetically unrelated antibiotics, neutramycin, and hygromycin A. Combining bioinformatic and chemical analyses, we identified the gene clusters responsible for antibiotic production. Interestingly, 2AW appears dissimilar from other cycloheximide producers in that the gene encoding the polyketide synthase resides on a separate part of the chromosome from the genes responsible for tailoring cycloheximide-specific modifications. This gene arrangement and our phylogenetic analyses of the gene products suggest that 2AW holds an evolutionarily ancestral lineage of the cycloheximide pathway. Our analyses support the hypothesis that the 2AW glutaramide gene cluster is basal to the lineage wherein cycloheximide production diverged from other glutarimide antibiotics. This study illustrates the power of combining modern biochemical and genomic analyses to gain insight into the evolution of antibiotic-producing microorganisms.
    Language English
    Publishing date 2016-05-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2016.00573
    Database MEDical Literature Analysis and Retrieval System OnLINE

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