Yeongseon Jang

Biotechnological procedures to select white rot fungi for the degradation of PAHs

White rot fungi are essential in forest ecology and are deeply involved in wood decomposition and the biodegradation of various xenobiotics. The fungal ligninolytic enzymes involved in these processes have recently become the focus of much attention for their possible biotechnological applications. Successful bioremediation requires the selection of species with desirable characteristics. In this study, 150 taxonomically and physiologically diverse white rot fungi, including 55 species, were investigated for their performance in a variety of biotechnological procedures, such as dye decolorization, gallic acid reaction, ligninolytic enzymes, and tolerance to four PAHs, phenanthrene, anthracene, fluoranthene, and pyrene. Among these fungi, six isolates showed the highest (>90%) tolerance to both individual PAH and mixed PAHs. And six isolates oxidized gallic acid with dark brown color and they rapidly decolorized RBBR within ten days. These fungi revealed various profiles when evaluated for their biotechnological performance to compare the capability of degradation of PAHs between two groups selected. As the results demonstrated the six best species selected from gallic acid more greatly degraded four PAHs than the other isolates selected via tolerance test. It provided that gallic acid reaction test can be performed to rank the fungi by their ability to degrade the PAHs. Most of all, Peniophora incarnata KUC8836 and Phlebia brevispora KUC9033 significantly degraded the four PAHs and can be considered prime candidates for the degradation of xenobiotic compounds in environmental settings.

Tunable Layer-by-Layer Polyelectrolyte Platforms for Comparative Cell Assays

We developed a cell-based assay based on the spin-assisted layer-by-layer (LbL) assembled polyelectrolyte matrix platforms. Three types of human breast epithelial cell lines including normal cells (184B5), noncancerous fibrocystic disease cells (MCF 10F), and metastatic cancerous cells (CAMA-1) were cultured, analyzed, and compared in parallel on various LbL-assembled polymer films. Poly(allylamine hydrochloride) (PAH) and poly(acrylic acid) (PAA) electrolyte polymers were used as the basic building units to form various LbL polyelectrolyte matrices. The mechanical rigidity, surface charge, and biorecognition property of the LbL platforms were controlled by tailoring the LbL surface, thermal cross-linking, and protein modification. Cellular phenotypic changes in adhesion, proliferation, and morphology on these LbL films were characterized and analyzed for the three different cell types. Our analysis results indicate that the cellular phenotype can be controlled by taking advantage of different surface charge, mechanical property, and biological modification (i.e., fibronectin in this case) of the LbL multilayer platforms. Importantly, cell phenotypical quantification results show that the cell spreading area per cell and optical density are useful parameters in distinguishing metastatic cancer cells from normal or fibrocystic disease cells on these LbL films. These LbL-based cell assay platforms have a potential for the development of various disease diagnostic cell assays.

Nanoparticle-Functionalized Polymer Platform for Controlling Metastatic Cancer Cell Adhesion, Shape, and Motility

Controlling and understanding the changes in metastatic cancer cell adhesion, shape, and motility are of paramount importance in cancer research, diagnosis, and treatment. Here, we used gold nanoparticles (AuNPs) as nanotopological structures and protein nanocluster forming substrates. Cell adhesion controlling proteins [in this case, fibronection (Fn) and ephrinB3] were modified to AuNPs, and these particles were then modified to the layer-by-layer (LbL) polymer surface that offers a handle for tuning surface charge and mechanical property of a cell-interfacing substrate. We found that metastatic cancer cell adhesion is affected by nanoparticle density on a surface, and ∼140 particles per 400 μm(2) (∼1.7 μm spacing between AuNPs) is optimal for effective metastatic cell adhesion. It was also shown that the AuNP surface density and protein nanoclustering on a spherical AuNP are controlling factors for the efficient interfacing and signaling of metastatic cancer cells. Importantly, the existence of nanotopological features (AuNPs in this case) is much more critical in inducing more dramatic changes in metastatic cell adhesion, protrusion, polarity, and motility than the presence of a cell adhesion protein, Fn, on the surface. Moreover, cell focal adhesion and motility-related paxillin clusters were heavily formed in cell lamellipodia and filopodia and high expression of phospho-paxillins were observed when the cells were cultured on either an AuNP or Fn-modified AuNP polymer surface. The ephrin signaling that results in the decreased expression of paxillin was found to be more effective when ephrins were modified to the AuNP surface than when ephrinB3 was directly attached to the polymer film. The overall trend for cell motility change is such that a nanoparticle-modified LbL surface induces higher cell motility and the AuNP modification to the LbL surface results in more pronounced change in cell motility than Fn or ephrin modification to the LbL surface.

Nanothin Coculture Membranes with Tunable Pore Architecture and Thermoresponsive Functionality for Transfer-Printable Stem Cell-Derived Cardiac Sheets

Coculturing stem cells with the desired cell type is an effective method to promote the differentiation of stem cells. The features of the membrane used for coculturing are crucial to achieving the best outcome. Not only should the membrane act as a physical barrier that prevents the mixing of the cocultured cell populations, but it should also allow effective interactions between the cells. Unfortunately, conventional membranes used for coculture do not sufficiently meet these requirements. In addition, cell harvesting using proteolytic enzymes following coculture impairs cell viability and the extracellular matrix (ECM) produced by the cultured cells. To overcome these limitations, we developed nanothin and highly porous (NTHP) membranes, which are ∼20-fold thinner and ∼25-fold more porous than the conventional coculture membranes. The tunable pore size of NTHP membranes at the nanoscale level was found crucial for the formation of direct gap junctions-mediated contacts between the cocultured cells. Differentiation of the cocultured stem cells was dramatically enhanced with the pore size-customized NTHP membrane system compared to conventional coculture methods. This was likely due to effective physical contacts between the cocultured cells and the fast diffusion of bioactive molecules across the membrane. Also, the thermoresponsive functionality of the NTHP membranes enabled the efficient generation of homogeneous, ECM-preserved, highly viable, and transfer-printable sheets of cardiomyogenically differentiated cells. The coculture platform developed in this study would be effective for producing various types of therapeutic multilayered cell sheets that can be differentiated from stem cells.

Phylogenetic analysis of major molds inhabiting woods and their discoloration characteristics. Part 1. Genus Trichoderma

Abstract The genus Trichoderma Persoon is a cosmopolitan genus consisting of more than 104 species and is commonly found on wood surfaces as a mold where it affects the appearance. Little attention has been given to wood-colonizing Trichoderma species and few studies are dedicated for identification of Trichoderma at the level of species. In the present study, up to 142 isolates were obtained from various wood samples. One Gliocladium and ten Trichoderma species were identified by morphological and molecular analysis. T. atroviride (30.3%) was the most abundant species followed by T. citrinoviride (26.8%) and T. harzianum (23.9%). The ability of Trichoderma species to discolor wood was also examined on sapwood blocks made of the commercially important radiata pine (Pinus radiata). T. pleuroticola caused the greatest discoloration of the wood surface.

Diversity of Wood-Inhabiting Polyporoid and Corticioid Fungi in Odaesan National Park, Korea

Abstract Polyporoid and corticioid fungi are among the most important wood-decay fungi. Not only do they contribute to nutrient cycling by decomposing wood debris, but they are also valuable sources for natural products. Polyporoid and corticioid wood-inhabiting fungi were investigated in Odaesan National Park. Fruit bodies were collected and identified based on morphological and molecular analyses using 28S and internal transcribed spacer regions of DNA sequences. As a result, a total of 149 species, 69 genera, 22 families, and 11 orders were recognized. Half (74 species) of the species were polypores, and the other half (75 species) were corticioid fungi. Most of the species belonged to Polyporales (92 species) followed by Hymenochaetales (33 species) and Russulales (11 species). At the genus level, a high number of species was observed from Steccherinum, Hyphodontia, Phanerochaete, Postia, and Trametes. Concerning distribution, almost all the species could be found below 1,000 m, and only 20% of the species were observed from above 1,000 m. Stereum subtomentosum, Trametes versicolor, T. hirsuta, T. pubescens, Bjerkandera adusta, and Ganoderma applanatum had wide distribution areas. Deciduous wood was the preferred substrate for the collected species. Sixty-three species were new to this region, and 21 species were new to Korea, of which 17 species were described and illustrated.

Comparison of the Diversity of Basidiomycetes from Dead Wood of the Manchurian fir (Abies holophylla) as Evaluated by Fruiting Body Collection, Mycelial Isolation, and 454 Sequencing

In this study, three different methods (fruiting body collection, mycelial isolation, and 454 sequencing) were implemented to determine the diversity of wood-inhabiting basidiomycetes from dead Manchurian fir (Abies holophylla). The three methods recovered similar species richness (26 species from fruiting bodies, 32 species from mycelia, and 32 species from 454 sequencing), but Fisher’s alpha, Shannon-Wiener, Simpson’s diversity indices of fungal communities indicated fruiting body collection and mycelial isolation displayed higher diversity compared with 454 sequencing. In total, 75 wood-inhabiting basidiomycetes were detected. The most frequently observed species were Heterobasidion orientale (fruiting body collection), Bjerkandera adusta (mycelial isolation), and Trichaptum fusco-violaceum (454 sequencing). Only two species, Hymenochaete yasudae and Hypochnicium karstenii, were detected by all three methods. This result indicated that Manchurian fir harbors a diverse basidiomycetous fungal community and for complete estimation of fungal diversity, multiple methods should be used. Further studies are required to understand their ecology in the context of forest ecosystems.

Screening for xylanase and β-xylosidase production from wood-inhabiting Penicillium strains for potential use in biotechnological applications.

Abstract Experiments were performed to find potential sources for enzyme production for the pulp and paper industry and for biological ethanol production by screening the cellulase, xylanase and β-xylosidase activities of 36 species of Penicillium isolated from various wood materials in Korea. Rice straw powder (RiceP), birchwood xylan (BirchX), and beechwood xylan (BeechX) were supplied as individual carbon sources for the Penicillium species. All Penicillium species tested in this study showed little cellulase activity, but some species exhibited remarkably high xylanase and β-xylosidase activities, as determined by a filter paper assay. P. oxalicum showed the greatest xylanase activity on RiceP (158.70 U ml-1). On the other hand, P. brevicompactum produced the highest active β-xylosidase on BirchX (6.25 U ml-1).

White-rot fungus Merulius tremellosus KUC9161 identified as an effective degrader of polycyclic aromatic hydrocarbons.

Polycyclic aromatic hydrocarbons (PAHs) have a highly recalcitrant structure; however, they can be degraded by white‐rot fungi which have the potential to biodegrade recalcitrant organic compounds. Four fungal isolates were selected from 23 newly isolated basidiomycetes, based on their dye decolorization rate, and they were evaluated for their ability to degrade 50 ppm of pyrene. The isolate phylogenetically affiliated to Merulius tremellosus KUC9161 demonstrated the highest degradation rate of pyrene, regardless of the production of ligninolytic enzyme activities. The selected isolates were tested for their ability to degrade pyrene and other PAHs in creosote‐contaminated soil. The results of the degradation tests indicated that M. tremellosus KUC9161 degraded a larger variety of PAH compounds than Phanerochaete chrysosporium, a known PAH degrader. On the basis of our results, the isolate M. tremellosus KUC9161 has a high potential to be used in the large‐scale biodegradation of PAHs, and the species may also be used to degrade recalcitrant materials in creosote‐contaminated soil.

Phylogenetic analysis and discoloration characteristics of major molds inhabiting woods. Part 3. Genus Cladosporium

Abstract The genus Cladosporium Link is one of the most well-known dark molds causing sapwood discoloration. Although the Cladosporium species are widespread in the world, little is known about the extent to which they stain wood. Twenty-eight isolates from seven different tree species in Korea were obtained and investigated in this study. Nine species, including three unknown Cladosporium species, were identified based on their genotypic characteristics. Cladosporium cladosporioides was the dominant species, followed by C. rectoides, C. perangustum, C. pseudocladosporioides, C. tenuissimum, and C. ramotenellum . Their discoloration ability was determined with sapwood blocks of Japanese red pine (Pinus densiflora) and radiata pine (Pinus radiata). On both blocks, Cladosporium tenuissimum and C. cladosporioides showed the highest level of discoloration.