Mark Marten - Academia.edu (original) (raw)

Papers by Mark Marten

Archives of Toxicology, Jul 27, 2020

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Fungal Genetics and Biology, Apr 1, 2019

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MBio, Feb 25, 2020

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TechConnect Briefs, May 8, 2005

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Proteomics, Oct 8, 2014

We describe the first phosphoproteome of the model filamentous fungus Aspergillus nidulans. Phosp... more We describe the first phosphoproteome of the model filamentous fungus Aspergillus nidulans. Phosphopeptides were enriched using titanium dioxide, separated using a convenient ultra-long reverse phase gradient, and identified using a "high-high" strategy (high mass accuracy on the parent and fragment ions) with higher-energy collisional dissociation. Using this approach 1801 phosphosites, from 1637 unique phosphopeptides, were identified. Functional classification revealed phosphoproteins were overrepresented under GO categories related to fungal morphogenesis: "sites of polar growth," "vesicle mediated transport," and "cytoskeleton organization." In these same GO categories, kinase-substrate analysis of phosphoproteins revealed the majority were target substrates of CDK and CK2 kinase families, indicating these kinase families play a prominent role in fungal morphogenesis. Kinase-substrate analysis also identified 57 substrates for kinases known to regulate secretion of hydrolytic enzymes (e.g. PkaA, SchA, and An-Snf1). Altogether this data will serve as a benchmark that can be used to elucidate regulatory networks functionally associated with fungal morphogenesis and secretion. All MS data have been deposited in the ProteomeXchange with identifier PXD000715 (http://proteomecentral.proteomexchange.org/dataset/PXD000715).

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Current Opinion in Biotechnology, Oct 1, 2008

Autophagy is a degradative process playing a role in both cell death and cell survival. Its prese... more Autophagy is a degradative process playing a role in both cell death and cell survival. Its presence is well conserved both in lower and higher eukaryotes. Recent studies have shown that activation or inhibition of autophagy may be possible in biotechnologically important species including mammalian cells and filamentous fungi using both environmental manipulation and genetic engineering. As our understanding of the autophagic biochemical pathways increases and monitoring methods become more user-friendly, the potential exists to obtain an optimum level of autophagy. This may allow for maximum cell survival and production of proteins and other metabolites in these industrially important eukaryotes.

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Journal of Proteome Research, Nov 6, 2002

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Biotechnology Progress, Oct 3, 1996

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Electrophoresis, Jul 1, 2002

Filamentous fungal fermentations are used to produce billions of dollars of biochemical and pharm... more Filamentous fungal fermentations are used to produce billions of dollars of biochemical and pharmaceutical products annually, yet are plagued by a number of poorly understood problems that would benefit from proteomic analysis. Unfortunately, few publications are available which describe extraction of filamentous fungal proteins for two-dimensional electrophoresis. The goal here was to develop protocols for extraction of fungal proteins, from both wild-type and a recombinant strain of the industrially important filamentous fungi Aspergillus oryzae, to be used for both one- and two-dimensional electrophoresis (1-DE and 2-DE). Because fungal cell walls are exceptionally resistant to fragmentation, four lysis protocols were tested: (i) boiling in strong alkali solution, (ii) boiling in Sodium dodecyl surfate (SDS), (iii) chemical lysis in Y-PER(R) reagent, and (iv) mechanical lysis via rapid agitation with glass beads in a Mini-BeadBeater(R). For both 1-DE and 2-DE, rapid agitation with glass beads was found to be the most efficient extraction method, yielding both mini- and large-format gels with little streaking or spot tailing, and proteins comprising a broad range of molecular weights and pI values.

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Applied and Environmental Microbiology, Feb 1, 2005

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Microbiology spectrum, Feb 2, 2022

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Advanced research in gastroenterology & hepatology, Jan 12, 2017

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Biotechnology Techniques, May 1, 1989

In a spheroplasting method which allows the fractionation and quantification of cloned invertase ... more In a spheroplasting method which allows the fractionation and quantification of cloned invertase activity in recombinantSaccharomyces cerevisiae cells, the yeast cell is selectively degraded with the enzyme Zymolyase for 60 minutes at 45°C to separate periplasmic proteins from cytoplasmic proteins. Most of the glucose-6-phosphate dehydrogenase (a cytoplasmic marker protein) was found in the cytoplasmic fraction.

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Chance, Sep 1, 2003

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Electrophoresis, Jul 1, 2002

While a variety of software packages are available for analyzing two-dimensional electrophoresis ... more While a variety of software packages are available for analyzing two-dimensional electrophoresis (2-DE) gel images, no comparisons between these packages have been published, making it difficult for end users to determine which package would best meet their needs. The goal here was to develop a set of tests to quantitatively evaluate and then compare two software packages, Melanie 3.0 and Z3, in three of the fundamental steps involved in 2-DE image analysis: (i) spot detection, (ii) gel matching, and (iii) spot quantitation. To test spot detection capability, automatically detected protein spots were compared to manually counted, "real" protein spots. Spot matching efficiency was determined by comparing distorted (both geometrically and nongeometrically) gel images with undistorted original images, and quantitation tests were performed on artificial gels with spots of varying Gaussian volumes. In spot detection tests, Z3 performed better than Melanie 3.0 and required minimal user intervention to detect approximately 89% of the actual protein spots and relatively few extraneous spots. Results from gel matching tests depended on the type of image distortion used. For geometric distortions, Z3 performed better than Melanie 3.0, matching 99% of the spots, even for extreme distortions. For nongeometrical distortions, both Z3 and Melanie 3.0 required user intervention and performed comparably, matching 95% of the spots. In spot quantitation tests, both Z3 and Melanie 3.0 predicted spot volumes relatively well for spot ratios less than 1:6. For higher ratios, Melanie 3.0 did much better. In summary, results suggest Z3 requires less user intervention than Melanie 3.0, thus simplifying differential comparison of 2-DE gel images. Melanie 3.0, however, offers many more optional tools for image editing, spot detection, data reporting and statistical analysis than Z3. All image files used for these tests and updated information on the software are available on the internet (http://www.umbc.edu/proteome), allowing similar testing of other 2-DE image analysis software packages.

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Biotechnology and Bioengineering, Jan 22, 2002

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Journal of Biotechnology, Apr 1, 1997

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Fungal Genetics and Biology, Sep 1, 2007

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Journal of Proteome Research, Apr 11, 2006

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Archives of Toxicology, Jul 27, 2020

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Fungal Genetics and Biology, Apr 1, 2019

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MBio, Feb 25, 2020

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TechConnect Briefs, May 8, 2005

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Proteomics, Oct 8, 2014

We describe the first phosphoproteome of the model filamentous fungus Aspergillus nidulans. Phosp... more We describe the first phosphoproteome of the model filamentous fungus Aspergillus nidulans. Phosphopeptides were enriched using titanium dioxide, separated using a convenient ultra-long reverse phase gradient, and identified using a "high-high" strategy (high mass accuracy on the parent and fragment ions) with higher-energy collisional dissociation. Using this approach 1801 phosphosites, from 1637 unique phosphopeptides, were identified. Functional classification revealed phosphoproteins were overrepresented under GO categories related to fungal morphogenesis: "sites of polar growth," "vesicle mediated transport," and "cytoskeleton organization." In these same GO categories, kinase-substrate analysis of phosphoproteins revealed the majority were target substrates of CDK and CK2 kinase families, indicating these kinase families play a prominent role in fungal morphogenesis. Kinase-substrate analysis also identified 57 substrates for kinases known to regulate secretion of hydrolytic enzymes (e.g. PkaA, SchA, and An-Snf1). Altogether this data will serve as a benchmark that can be used to elucidate regulatory networks functionally associated with fungal morphogenesis and secretion. All MS data have been deposited in the ProteomeXchange with identifier PXD000715 (http://proteomecentral.proteomexchange.org/dataset/PXD000715).

Bookmarks Related papers MentionsView impact

Current Opinion in Biotechnology, Oct 1, 2008

Autophagy is a degradative process playing a role in both cell death and cell survival. Its prese... more Autophagy is a degradative process playing a role in both cell death and cell survival. Its presence is well conserved both in lower and higher eukaryotes. Recent studies have shown that activation or inhibition of autophagy may be possible in biotechnologically important species including mammalian cells and filamentous fungi using both environmental manipulation and genetic engineering. As our understanding of the autophagic biochemical pathways increases and monitoring methods become more user-friendly, the potential exists to obtain an optimum level of autophagy. This may allow for maximum cell survival and production of proteins and other metabolites in these industrially important eukaryotes.

Bookmarks Related papers MentionsView impact

Journal of Proteome Research, Nov 6, 2002

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Biotechnology Progress, Oct 3, 1996

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Electrophoresis, Jul 1, 2002

Filamentous fungal fermentations are used to produce billions of dollars of biochemical and pharm... more Filamentous fungal fermentations are used to produce billions of dollars of biochemical and pharmaceutical products annually, yet are plagued by a number of poorly understood problems that would benefit from proteomic analysis. Unfortunately, few publications are available which describe extraction of filamentous fungal proteins for two-dimensional electrophoresis. The goal here was to develop protocols for extraction of fungal proteins, from both wild-type and a recombinant strain of the industrially important filamentous fungi Aspergillus oryzae, to be used for both one- and two-dimensional electrophoresis (1-DE and 2-DE). Because fungal cell walls are exceptionally resistant to fragmentation, four lysis protocols were tested: (i) boiling in strong alkali solution, (ii) boiling in Sodium dodecyl surfate (SDS), (iii) chemical lysis in Y-PER(R) reagent, and (iv) mechanical lysis via rapid agitation with glass beads in a Mini-BeadBeater(R). For both 1-DE and 2-DE, rapid agitation with glass beads was found to be the most efficient extraction method, yielding both mini- and large-format gels with little streaking or spot tailing, and proteins comprising a broad range of molecular weights and pI values.

Bookmarks Related papers MentionsView impact

Applied and Environmental Microbiology, Feb 1, 2005

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Microbiology spectrum, Feb 2, 2022

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Advanced research in gastroenterology & hepatology, Jan 12, 2017

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Biotechnology Techniques, May 1, 1989

In a spheroplasting method which allows the fractionation and quantification of cloned invertase ... more In a spheroplasting method which allows the fractionation and quantification of cloned invertase activity in recombinantSaccharomyces cerevisiae cells, the yeast cell is selectively degraded with the enzyme Zymolyase for 60 minutes at 45°C to separate periplasmic proteins from cytoplasmic proteins. Most of the glucose-6-phosphate dehydrogenase (a cytoplasmic marker protein) was found in the cytoplasmic fraction.

Bookmarks Related papers MentionsView impact

Chance, Sep 1, 2003

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Electrophoresis, Jul 1, 2002

While a variety of software packages are available for analyzing two-dimensional electrophoresis ... more While a variety of software packages are available for analyzing two-dimensional electrophoresis (2-DE) gel images, no comparisons between these packages have been published, making it difficult for end users to determine which package would best meet their needs. The goal here was to develop a set of tests to quantitatively evaluate and then compare two software packages, Melanie 3.0 and Z3, in three of the fundamental steps involved in 2-DE image analysis: (i) spot detection, (ii) gel matching, and (iii) spot quantitation. To test spot detection capability, automatically detected protein spots were compared to manually counted, "real" protein spots. Spot matching efficiency was determined by comparing distorted (both geometrically and nongeometrically) gel images with undistorted original images, and quantitation tests were performed on artificial gels with spots of varying Gaussian volumes. In spot detection tests, Z3 performed better than Melanie 3.0 and required minimal user intervention to detect approximately 89% of the actual protein spots and relatively few extraneous spots. Results from gel matching tests depended on the type of image distortion used. For geometric distortions, Z3 performed better than Melanie 3.0, matching 99% of the spots, even for extreme distortions. For nongeometrical distortions, both Z3 and Melanie 3.0 required user intervention and performed comparably, matching 95% of the spots. In spot quantitation tests, both Z3 and Melanie 3.0 predicted spot volumes relatively well for spot ratios less than 1:6. For higher ratios, Melanie 3.0 did much better. In summary, results suggest Z3 requires less user intervention than Melanie 3.0, thus simplifying differential comparison of 2-DE gel images. Melanie 3.0, however, offers many more optional tools for image editing, spot detection, data reporting and statistical analysis than Z3. All image files used for these tests and updated information on the software are available on the internet (http://www.umbc.edu/proteome), allowing similar testing of other 2-DE image analysis software packages.

Bookmarks Related papers MentionsView impact

Biotechnology and Bioengineering, Jan 22, 2002

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Journal of Biotechnology, Apr 1, 1997

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Fungal Genetics and Biology, Sep 1, 2007

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Journal of Proteome Research, Apr 11, 2006

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