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105. Cornification of nail keratinocytes requires autophagy for bulk degradation of intracellular proteins while sparing components of the cytoskeleton

Author

Jaeger, Karin, primary, Sukseree, Supawadee, additional, Zhong, Shaomin, additional, Phinney, Brett S., additional, Mlitz, Veronika, additional, Buchberger, Maria, additional, Narzt, Marie Sophie, additional, Gruber, Florian, additional, Tschachler, Erwin, additional, Rice, Robert H., additional, and Eckhart, Leopold, additional

Published
2018
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106. Assessing probe-specific dye and slide biases in two-color microarray data

Author

Goldberg Zelanna, Rice Robert H, Jia Yi, Phetsom Jirapa, Jung Kihong, Dardick Chris, Shultz Michael, Lee Geun-Cheol, Lu Ruixiao, Schnable Patrick S, Ronald Pamela, and Rocke David M

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background A primary reason for using two-color microarrays is that the use of two samples labeled with different dyes on the same slide, that bind to probes on the same spot, is supposed to adjust for many factors that introduce noise and errors into the analysis. Most users assume that any differences between the dyes can be adjusted out by standard methods of normalization, so that measures such as log ratios on the same slide are reliable measures of comparative expression. However, even after the normalization, there are still probe specific dye and slide variation among the data. We define a method to quantify the amount of the dye-by-probe and slide-by-probe interaction. This serves as a diagnostic, both visual and numeric, of the existence of probe-specific dye bias. We show how this improved the performance of two-color array analysis for arrays for genomic analysis of biological samples ranging from rice to human tissue. Results We develop a procedure for quantifying the extent of probe-specific dye and slide bias in two-color microarrays. The primary output is a graphical diagnostic of the extent of the bias which called ECDF (Empirical Cumulative Distribution Function), though numerical results are also obtained. Conclusion We show that the dye and slide biases were high for human and rice genomic arrays in two gene expression facilities, even after the standard intensity-based normalization, and describe how this diagnostic allowed the problems causing the probe-specific bias to be addressed, and resulted in important improvements in performance. The R package LMGene which contains the method described in this paper has been available to download from Bioconductor.

Published
2008
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108. Proteomic analysis of hair shafts from monozygotic twins: Expression profiles and genetically variant peptides.

Author

Wu, Pei-Wen, Wu, Pei-Wen, Mason, Katelyn E, Durbin-Johnson, Blythe P, Salemi, Michelle, Phinney, Brett S, Rocke, David M, Parker, Glendon J, Rice, Robert H, Wu, Pei-Wen, Wu, Pei-Wen, Mason, Katelyn E, Durbin-Johnson, Blythe P, Salemi, Michelle, Phinney, Brett S, Rocke, David M, Parker, Glendon J, and Rice, Robert H

Abstract

Forensic association of hair shaft evidence with individuals is currently assessed by comparing mitochondrial DNA haplotypes of reference and casework samples, primarily for exclusionary purposes. Present work tests and validates more recent proteomic approaches to extract quantitative transcriptional and genetic information from hair samples of monozygotic twin pairs, which would be predicted to partition away from unrelated individuals if the datasets contain identifying information. Protein expression profiles and polymorphic, genetically variant hair peptides were generated from ten pairs of monozygotic twins. Profiling using the protein tryptic digests revealed that samples from identical twins had typically an order of magnitude fewer protein expression differences than unrelated individuals. The data did not indicate that the degree of difference within twin pairs increased with age. In parallel, data from the digests were used to detect genetically variant peptides that result from common nonsynonymous single nucleotide polymorphisms in genes expressed in the hair follicle. Compilation of the variants permitted sorting of the samples by hierarchical clustering, permitting accurate matching of twin pairs. The results demonstrate that genetic differences are detectable by proteomic methods and provide a framework for developing quantitative statistical estimates of personal identification that increase the value of hair shaft evidence.

Published
2017

110. Views of Our Readers

Author

Howard, Earl E., Walker, Thomas F., Wilson, Wesley T., Williams, Ira Jewell, Rice, Robert H., McLaren, W. G., Hallows, E. H., Burkhard, Myron J., and Cooper, Drury W.

Published
1949

112. Relationship between the molecular composition, visible light absorption, and health-related properties of smoldering woodsmoke aerosols.

Author

Lam Kam Chan, Nguyen, Khanh Q., Karim, Noreen, Yatian Yang, Rice, Robert H., He, Guochun, Denison, Michael S., and Nguyen, Tran B.

Abstract

Organic aerosols generated from the smoldering combustion of wood critically impact air quality and health for billions of people worldwide; yet, the links between the chemical components and the optical or biological effects of woodsmoke aerosols (WSA) are still poorly understood. In this work, an untargeted analysis of the molecular composition of smoldering WSA, generated in a controlled environment from nine types of heartwood fuels (African Mahogany, Birch, Cherry, Maple, Pine, Poplar, Red Oak, Redwood, and Walnut) identified several hundred compounds using gas chromatography mass spectrometry (GC-MS) and nano-electrospray high-resolution mass spectrometry (HRMS) with tandem multistage mass spectrometry (MSn). The effects of WSA on cell toxicity, aryl hydrocarbon receptor (AhR)- and estrogen receptor (ER)-dependent gene expression were characterized with cellular assays, and the visible mass absorption coefficients (MACvis) of WSA were measured with UV-visible spectroscopy. The WSA studied in this work have significant levels of biological and toxicological activity, with exposure levels in both an outdoor and indoor environment similar to or greater than those of other toxicants. A correlation between the HRMS molecular composition and aerosol properties found that phenolic compounds from the oxidative decomposition of lignin were the main drivers of aerosol effects, while the cellulose decomposition products played a secondary role, e.g., levoglucosan was anti-correlated with multiple effects. Polycyclic aromatic hydrocarbons (PAHs) were not expected to form at the combustion temperature in this work, nor were observed above the detection limit; thus, biological and optical properties of the smoldering WSA are not attributed to PAHs. Syringyl compounds tend to correlate with cell toxicity, while the more conjugated molecules (including several compounds assigned to dimers) had higher AhR activity and MACvis. The negative correlation between cell toxicity and AhR activity suggests that the toxicity of WSA to cells was not mediated by the AhR. Both mass-normalized biological outcomes had a statistically-significant dependence on the degree of combustion of the wood. In addition, our observations support that the visible light absorption of WSA is at least partially due to charge transfer effects in aerosols, as previously suggested. Finally, MACvis had no correlation with toxicity or receptor signaling, suggesting that key chromophores are not biologically active on the endpoints tested. [ABSTRACT FROM AUTHOR]

Published
2019
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115. Correction: A keratin scaffold regulates epidermal barrier formation, mitochondrial lipid composition, and activity

Author

Kumar, Vinod, primary, Bouameur, Jamal-Eddine, additional, Bär, Janina, additional, Rice, Robert H., additional, Hornig-Do, Hue-Tran, additional, Roop, Dennis R., additional, Schwarz, Nicole, additional, Brodesser, Susanne, additional, Thiering, Sören, additional, Leube, Rudolf E., additional, Wiesner, Rudolf J., additional, Vijayaraj, Preethi, additional, Brazel, Christina B., additional, Heller, Sandra, additional, Binder, Hans, additional, Löffler-Wirth, Henry, additional, Seibel, Peter, additional, and Magin, Thomas M., additional

Published
2016
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116. Proteomic Analysis of Hair Shaft and Nail Plate

Author

Rice, Robert H.

Subjects
Proteomics, integumentary system, Gene Expression Regulation, Nails, Gene Expression Profiling, Humans, Article, Hair
Abstract

The protein components of living cells in the hair follicle are amenable to study by standard molecular biological techniques, but identifying those in the hair shaft has been problematic until recently. Most of the protein, primarily keratins and keratin associated proteins, can be extracted under denaturing conditions, but 15–20% is intractable due to transglutaminase-mediated cross-linking. Shotgun proteomics now permits identifying >300 constituents of the isopeptide cross-linked proteome and even certain post-translational modifications. The proteins originate from all the intracellular compartments, indicating that the cross-linking process makes effective use of available resources to produce structures with great mechanical stability. Knowing this proteome provides a foundation for correlating defects in hair shaft structure with protein deficiencies. Such investigations can be extended to mouse models of aberrant pelage hair. Thus, inbred mouse strains can be distinguished by their hair proteomes, raising the possibility of similar variation in the human population. The nail plate is also amenable to this shotgun proteomic approach. Providing discrete and noninvasive sampling of the human proteome, these epidermal appendages could have diagnostic utility for certain disease states.

Published
2011

117. Parallel responses of human epidermal keratinocytes to inorganic SbIII and AsIII.

Author

Phillips, Marjorie A., Cánovas, Angela, Pei-Wen Wu, Islas-Trejo, Alma, Medrano, Juan F., and Rice, Robert H.

Subjects
ANTIMONY, CARCINOGENICITY, KERATINOCYTES
Abstract

SbsupIII and AssupIII are known to exhibit similar chemical properties, but the degree of similarity in their effects on biological systems merits further exploration. The present work compares the responses of human epidermal keratinocytes, a known target cell type for arsenite-induced carcinogenicity, to these metalloids after treatment for 1 week at environmentally relevant concentrations. Previous work with these cells has shown that arsenite and antimonite have parallel effects in suppressing differentiation, altering levels of several critical enzymes and maintaining colony-forming ability. More globally, protein profiling now reveals parallels in SbsupIII and AssupIII effects. The more sensitive technique of transcriptional profiling also shows considerable parallels. Thus, gene expression changes were almost entirely in the same directions for the two treatments, although the degree of change was sometimes significantly different. Inspection of the changes revealed that RYR1 and LRIG1 were among the genes strongly suppressed, consistent with reduced calciumdependent differentiation and maintenance of epidermal growth factor-dependent proliferative potential. Moreover, levels of microRNAs in the cells were altered in parallel, with nearly 90% of the 198 most highly expressed ones being suppressed. Among these was miR-203, which is known to decrease proliferative potential. Finally, both SbsupIII and AssupIII were seen to attenuate bone morphogenetic protein 6 induction of dual-specificity phosphatases 2 and 14, consistent with maintaining epidermal growth factor receptor signalling. These findings raise the question of whether SbsupIII, like AssupIII, could act as a human skin carcinogen. [ABSTRACT FROM AUTHOR]

Published
2016
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129. Human Proteinpedia enables sharing of human protein data

Author

Mathivanan, Suresh, primary, Ahmed, Mukhtar, additional, Ahn, Natalie G, additional, Alexandre, Hainard, additional, Amanchy, Ramars, additional, Andrews, Philip C, additional, Bader, Joel S, additional, Balgley, Brian M, additional, Bantscheff, Marcus, additional, Bennett, Keiryn L, additional, Björling, Erik, additional, Blagoev, Blagoy, additional, Bose, Ron, additional, Brahmachari, Samir K, additional, Burlingame, Alma S, additional, Bustelo, Xosé R, additional, Cagney, Gerard, additional, Cantin, Greg T, additional, Cardasis, Helene L, additional, Celis, Julio E, additional, Chaerkady, Raghothama, additional, Chu, Feixia, additional, Cole, Philip A, additional, Costello, Catherine E, additional, Cotter, Robert J, additional, Crockett, David, additional, DeLany, James P, additional, De Marzo, Angelo M, additional, DeSouza, Leroi V, additional, Deutsch, Eric W, additional, Dransfield, Eric, additional, Drewes, Gerard, additional, Droit, Arnaud, additional, Dunn, Michael J, additional, Elenitoba-Johnson, Kojo, additional, Ewing, Rob M, additional, Eyk, Jennifer Van, additional, Faca, Vitor, additional, Falkner, Jayson, additional, Fang, Xiangming, additional, Fenselau, Catherine, additional, Figeys, Daniel, additional, Gagné, Pierre, additional, Gelfi, Cecilia, additional, Gevaert, Kris, additional, Gimble, Jeffrey M, additional, Gnad, Florian, additional, Goel, Renu, additional, Gromov, Pavel, additional, Hanash, Samir M, additional, Hancock, William S, additional, Harsha, HC, additional, Hart, Gerald, additional, Hays, Faith, additional, He, Fuchu, additional, Hebbar, Prashantha, additional, Helsens, Kenny, additional, Hermeking, Heiko, additional, Hide, Winston, additional, Hjernø, Karin, additional, Hochstrasser, Denis F, additional, Hofmann, Oliver, additional, Horn, David M, additional, Hruban, Ralph H, additional, Ibarrola, Nieves, additional, James, Peter, additional, Jensen, Ole N, additional, Jensen, Pia Hønnerup, additional, Jung, Peter, additional, Kandasamy, Kumaran, additional, Kheterpal, Indu, additional, Kikuno, Reiko F, additional, Korf, Ulrike, additional, Körner, Roman, additional, Kuster, Bernhard, additional, Kwon, Min-Seok, additional, Lee, Hyoung-Joo, additional, Lee, Young-Jin, additional, Lefevre, Michael, additional, Lehvaslaiho, Minna, additional, Lescuyer, Pierre, additional, Levander, Fredrik, additional, Lim, Megan S, additional, Löbke, Christian, additional, Loo, Joseph A, additional, Mann, Matthias, additional, Martens, Lennart, additional, Martinez-Heredia, Juan, additional, McComb, Mark, additional, McRedmond, James, additional, Mehrle, Alexander, additional, Menon, Rajasree, additional, Miller, Christine A, additional, Mischak, Harald, additional, Mohan, S Sujatha, additional, Mohmood, Riaz, additional, Molina, Henrik, additional, Moran, Michael F, additional, Morgan, James D, additional, Moritz, Robert, additional, Morzel, Martine, additional, Muddiman, David C, additional, Nalli, Anuradha, additional, Navarro, J Daniel, additional, Neubert, Thomas A, additional, Ohara, Osamu, additional, Oliva, Rafael, additional, Omenn, Gilbert S, additional, Oyama, Masaaki, additional, Paik, Young-Ki, additional, Pennington, Kyla, additional, Pepperkok, Rainer, additional, Periaswamy, Balamurugan, additional, Petricoin, Emanuel F, additional, Poirier, Guy G, additional, Prasad, T S Keshava, additional, Purvine, Samuel O, additional, Rahiman, B Abdul, additional, Ramachandran, Prasanna, additional, Ramachandra, Y L, additional, Rice, Robert H, additional, Rick, Jens, additional, Ronnholm, Ragna H, additional, Salonen, Johanna, additional, Sanchez, Jean-Charles, additional, Sayd, Thierry, additional, Seshi, Beerelli, additional, Shankari, Kripa, additional, Sheng, Shi Jun, additional, Shetty, Vivekananda, additional, Shivakumar, K, additional, Simpson, Richard J, additional, Sirdeshmukh, Ravi, additional, Michael Siu, K W, additional, Smith, Jeffrey C, additional, Smith, Richard D, additional, States, David J, additional, Sugano, Sumio, additional, Sullivan, Matthew, additional, Superti-Furga, Giulio, additional, Takatalo, Maarit, additional, Thongboonkerd, Visith, additional, Trinidad, Jonathan C, additional, Uhlen, Mathias, additional, Vandekerckhove, Joël, additional, Vasilescu, Julian, additional, Veenstra, Timothy D, additional, Vidal-Taboada, José-Manuel, additional, Vihinen, Mauno, additional, Wait, Robin, additional, Wang, Xiaoyue, additional, Wiemann, Stefan, additional, Wu, Billy, additional, Xu, Tao, additional, Yates, John R, additional, Zhong, Jun, additional, Zhou, Ming, additional, Zhu, Yunping, additional, Zurbig, Petra, additional, and Pandey, Akhilesh, additional

Published
2008
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139. Lce1Family Members Are Nrf2-Target Genes that Are Induced to Compensate for the Loss of Loricrin

Author

Ishitsuka, Yosuke, Huebner, Aaron J., Rice, Robert H., Koch, Peter J., Speransky, Vladislav V., Steven, Alasdair C., and Roop, Dennis R.

Abstract

Loricrin is a major component of the cornified cell envelope, a highly insoluble structure composed of covalently cross-linked proteins. Although loricrin knockout mice only exhibit a mild transient phenotype at birth, they show a marked delay in the formation of an epidermal barrier in utero. We recently discovered that induction of a compensatory response to repair the defective barrier is initiated by amniotic fluid via activation of NF-E2-related factor 2 and identified Sprr2dand Sprr2has direct transcriptional targets. Proteomic analysis suggested that other proteins were also incorporated into the loricrin knockout cell envelope, in addition to the small proline rich proteins. Here we present evidence suggesting that the late cornified envelope 1 proteins are also compensatory components as determined by their localization within the loricrin knockout cell envelope via immunoelectron microscopy. We also demonstrate that late cornified envelope 1 genes are upregulated at the transcriptional level in loricrin knockout mouse skin and confirm that late cornified envelope 1 genes are transcriptional targets of NRF2. Our present study further highlights the complexity and importance of a compensatory mechanism that evolved in terrestrial animals to ensure the formation of a functional epidermal barrier.

Published
2016
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144. Derivation and Osmotolerance Characterization of Three Immortalized Tilapia (Oreochromis mossambicus) Cell Lines.

Author

Gardell, Alison M., Qin, Qin, Rice, Robert H., Li, Johnathan, and Kültz, Dietmar

Subjects
MOZAMBIQUE tilapia, TILAPIA, FISH physiology, CELL lines, CELL culture
Abstract

Fish cell cultures are becoming more widely used models for investigating molecular mechanisms of physiological response to environmental challenge. In this study, we derived two immortalized Mozambique tilapia (Oreochromis mossambicus) cell lines from brain (OmB) and lip epithelium (OmL), and compared them to a previously immortalized bulbus arteriosus (TmB) cell line. The OmB and OmL cell lines were generated without or with Rho-associated kinase (ROCK) inhibitor/3T3 feeder layer supplementation. Although both approaches were successful, ROCK inhibitor/feeder layer supplementation was found to offer the advantages of selecting for epithelial-like cell type and decreasing time to immortalization. After immortalization (≥ passage 5), we characterized the proteomes of the newly derived cell lines (OmB and OmL) using LCMS and identified several unique cell markers for each line. Subsequently, osmotolerance for each of the three cell lines following acute exposure to elevated sodium chloride was evaluated. The acute maximum osmotolerance of these tilapia cell lines (>700 mOsm/kg) was markedly higher than that of any other known vertebrate cell line, but was significantly higher in the epithelial-like OmL cell line. To validate the physiological relevance of these tilapia cell lines, we quantified the effects of acute hyperosmotic challenge (450 mOsm/kg and 700 mOsm/kg) on the transcriptional regulation of two enzymes involved in biosynthesis of the compatible organic osmolyte, myo-inositol. Both enzymes were found to be robustly upregulated in all three tilapia cell lines. Therefore, the newly established tilapia cells lines represent valuable tools for studying molecular mechanisms involved in the osmotic stress response of euryhaline fish. [ABSTRACT FROM AUTHOR]

Published
2014
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