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Sean P Palecek

Publications and source records attributed to Sean P Palecek.

At least 19 recordsLinked to original sources
PubMed2006

Analyzing the dose-dependence of the Saccharomyces cerevisiae global transcriptional response to methyl methanesulfonate and ionizing radiation.

BACKGROUND: One of the most crucial tasks for a cell to ensure its long term survival is preserving the integrity of its genetic heritage via maintenance of DNA structure and sequence. While the DNA damage response in the yeast Saccharomyces cerevisiae, a model eukaryotic organism, has been extensively studied, much remains to be elucidated about how the organism senses and responds to different types and doses of DNA damage. We have measured the global transcriptional response of S. cerevisiae to multiple doses of two representative DNA damaging agents, methyl methanesulfonate (MMS) and gamma radiation. RESULTS: Hierarchical clustering of genes with a statistically significant change in transcription illustrated the differences in the cellular responses to MMS and gamma radiation. Overall, MMS produced a larger transcriptional response than gamma radiation, and many of the genes modulated in response to MMS are involved in protein and translational regulation. Several clusters of coregulated genes whose responses varied with DNA damaging agent dose were identified. Perhaps the most interesting cluster contained four genes exhibiting biphasic induction in response to MMS dose. All of the genes (DUN1, RNR2, RNR4, and HUG1) are involved in the Mec1p kinase pathway known to respond to MMS, presumably due to stalled DNA replication forks. The biphasic responses of these genes suggest that the pathway is induced at lower levels as MMS dose increases. The genes in this cluster with a threefold or greater transcriptional response to gamma radiation all showed an increased induction with increasing gamma radiation dosage. CONCLUSION: Analyzing genome-wide transcriptional changes to multiple doses of external stresses enabled the identification of cellular responses that are modulated by magnitude of the stress, providing insights into how a cell deals with genotoxicity.

DNA Damage↗
PubMed2006

Antifungal activity from 14-helical beta-peptides.

We have discovered that short beta-peptides (9 or 10 residues) designed to adopt globally amphiphilic helical conformations display significant antifungal activity. The most promising beta-peptides cause little lysis of human red blood cells at concentrations that kill Candida albicans, a common human fungal pathogen. Since fungi are eukaryotes, discrimination between fungal and human cells is a significant finding. Our beta-peptides are active under assay conditions that mimic physiological ionic strength; in contrast, alpha-helix-forming host-defense alpha-peptides are inactive against C. albicans under these conditions.

Antifungal Agents↗
PubMed2006

3-D microwell culture of human embryonic stem cells.

Human embryonic stem cells (hESCs) have the ability to proliferate indefinitely and differentiate into each of the embryonic cell lineages. Great care is required to maintain undifferentiated hESC cultures since spontaneous differentiation often occurs in culture, presumably resulting from soluble factors, cell-cell contact, and/or cell-matrix signaling. hESC differentiation is typically stimulated via generation of embryoid bodies (EBs) and lineage commitment of individual cells depends upon numerous cues throughout the EB environment, including EB shape and size. Common EB formation protocols, however, produce a very heterogeneous size distribution, perhaps reducing efficiency of directed differentiation. We have developed a 3-D microwell-based method to maintain undifferentiated hESC cultures for weeks without passaging using physical and extracellular matrix patterning constraints to limit colony growth. Over 90% of hESCs cultured in microwells for 2-3 weeks were viable and expressed the hESC transcription marker Oct-4. Upon passaging to Matrigel-coated tissue culture-treated polystyrene dishes (TCPS), microwell cultured hESCs maintained undifferentiated proliferation. Microwell culture also permits formation of hESC colonies with a defined size, which can then be used to form monodisperse EBs. When cultured in this system, hESCs retained pluripotency and self-renewal, and were able to be passaged to standard unconstrained culture conditions.

Biocompatible Materials↗
PubMed2006

Photocleavable peptide hydrogel arrays for MALDI-TOF analysis of kinase activity.

We have developed an acrylamide copolymerization strategy to immobilize acrylamide labeled peptides and proteins into a hydrogel surface and detect their modifications using MALDI-TOF mass spectrometry. Copolymerization into hydrogels is robust, compatible with "off-the-shelf" chemistry, and yields materials and surfaces that are stable to aqueous or organic solvents, drying, high or low temperature, high or low pH, oxidizing agents, sonication, mechanical contact, etc. The use of acrylamide hydrogels allows immobilization of substrates in a hydrated environment that can be used both as a biological reaction matrix and as a MALDI target. In our strategy, a substrate peptide was designed in a modular fashion to include both modification site and affinity domains. It was labeled with an acrylamide functionality using a generalized chemistry and covalently attached to the surface with a photocleavable linker, allowing for aggressive washing to remove any fouling, followed by selective release for MALDI-TOF analysis. Using this system we were able to analyze and compare v-Abl (truncated) and c-Abl (full-length) kinase activity on a peptide substrate with an affinity domain specific for the full-length kinase, observing excellent overall reproducibility in the extent of phosphorylation detected. This work serves as proof of principle for modular substrate design strategies for mass spectrometry-readable biosensors.

Acrylamides↗
PubMed2006

Inhibition of human embryonic stem cell differentiation by mechanical strain.

Mechanical forces have been reported to induce proliferation and/or differentiation in many cell types, but the role of mechanotransduction during embryonic stem cell fate decisions is unknown. To ascertain the role of mechanical strain in human embryonic stem cell (hESC) differentiation, we measured the rate of hESC differentiation in the presence and absence of biaxial cyclic strain. Above a threshold of 10% cyclic strain, applied to a deformable elastic substratum upon which the hESC colonies were cultured, hESC differentiation was reduced and self-renewal was promoted without selecting against survival of differentiated or undifferentiated cells. Frequency of mechanical strain application had little effect on extent of differentiation. hESCs cultured under cyclic strain retained pluripotency, evidenced by their ability to differentiate to cell lineages in all three germ layers. Mechanical inhibition of hESC differentiation could not be traced to secretion of chemical factors into the media suggesting that mechanical forces may directly regulate hESC differentiation. Mechanical strain is not sufficient to inhibit differentiation, however, in unconditioned medium, hESCs grown under strain differentiated at the same rate as cells cultured in the absence of strain. Thus, while mechanical forces play a role in regulating hESC self-renewal and differentiation, they must act synergistically with chemical signals. These findings imply that application of mechanical forces may be useful, in combination with chemical and matrix-encoded signals, towards controlling differentiation of hESCs for therapeutic applications.

Cell Culture Techniques↗
PubMed2006

Generation and differentiation of human embryonic stem cell-derived keratinocyte precursors.

Human embryonic stem cells (hESC) hold tremendous potential in the future of tissue engineering, offering promise as a source of virtually unlimited quantities of desired cell and tissue types. We have identified soluble chemical and extracellular matrix factors that permit isolation of keratinocyte precursors from hESCs. Culturing embryoid bodies (EB) formed from hESCs in a defined serum-free keratinocyte growth medium on a gelatin matrix generated keratin 14 (K14) expressing cells with an epithelial morphology. These K14 expressing cells could be subcultured in medium supplemented with hydrocortisone and induced to stratify and terminally differentiate by addition of calcium. Optimum times for obtaining K14 expressing cells were found for EB formation and for differentiation and growth of cultures after EB plating. EB formation was not necessary to generate keratinocyte precursors; direct transfer of hESC colonies to keratinocyte growth medium permitted differentiation into the keratinocyte lineage. With further studies to optimize generation and purification of hESC-derived keratinocyte precursors, these cells could provide a source of epidermal cells for skin tissue engineering applications in vitro or in vivo.

Biomarkers↗
PubMed2005

Disruption of LRG1 inhibits mother-daughter separation in Saccharomyces cerevisiae.

LRG1, previously characterized as a Rho-GAP that regulates beta-1,3-glucan synthesis, was identified using a filtration screen designed to isolate genes that promote cell aggregation in Sigma1278b Saccharomyces cerevisiae. Disruption of LRG1 in haploid cells resulted in enhanced invasive growth and a strain-specific 'clustered' phenotype that is a consequence of failed separation of mother and daughter cells. Genetic analysis revealed that clustering required functional ROM2, FKS1 and STE12 but not FLO8 or FLO11. Additionally, this phenotype required sufficient nitrogen. beta-1,3-Glucan content was elevated in lrg1 haploids and these cells possessed a thicker cell wall and septum than wild-type strains. Additional glucan at the bud site inhibited separation of lrg1 mutants as the clustered phenotype was repressed by expression of the glucanases ENG1 or EGT2.

Cell Adhesion↗
PubMed2005

Platelet cryopreservation using a trehalose and phosphate formulation.

Long-term storage of platelets is infeasible due to platelet activation at low temperatures. In an effort to address this problem, we evaluated the effectiveness of a formulation combining trehalose and phosphate in protecting platelet structure and function following cryopreservation. An annexin V binding assay was used to quantify the efficacy of the trehalose and phosphate formulation in suppressing platelet activation during cryopreservation. Of the platelets cryopreserved with the trehalose plus phosphate formulation, 23% +/- 1.2% were nonactivated, compared with 9.8% +/- 0.26% nonactivated following cryopreservation with only trehalose. The presence of both trehalose and phosphate in the cryopreservation medium is critical for cell survival and preincubation in trehalose plus phosphate solutions further enhances viability. The effectiveness of trehalose plus phosphate in preserving platelets in a nonactivated state is comparable to 6% dimethyl sulfoxide (Me(2)SO). Measurements of platelet metabolic activity using an alamarBlue assay also established that trehalose plus phosphate is superior to trehalose alone. Finally, platelets protected by the trehalose plus phosphate formulation exhibit similar aggregation response upon thrombin addition as fresh platelets, but an increase of cytosolic calcium concentration upon thrombin addition was not observed in the cryopreserved platelets. These results suggest that trehalose and phosphate protect several aspects of platelet structure and function during cryopreservation, including an intact plasma membrane, metabolic activity, and aggregation in response to thrombin, but not intracellular calcium release in response to thrombin.

Annexin A5↗
PubMed2005

Phase behavior of freeze-dried phospholipid-cholesterol mixtures stabilized with trehalose.

A study is presented of the role of cholesterol content on the gel-to-liquid crystalline phase transition of freeze-dried liposomes stabilized with trehalose, a well known lyoprotectant. The phospholipids considered in this work, DPPC and DPPE, belong to the two predominant phospholipid species found in numerous biological membranes. Cholesterol is found in abundance in mammalian plasma membranes. DSC measurements reveal that cholesterol-containing liposomes exhibit multiple phase transitions upon dehydration. Addition of trehalose to these systems lowers the phase transition temperature and limits the phase separation of the lipidic components upon freeze-drying. This work provides strong evidence for the effectiveness of trehalose in stabilizing cholesterol-containing membranes upon lyophilization.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2004

Cryopreservation of adherent human embryonic stem cells.

Standard human embryonic stem (HES) cell cryopreservation methodologies, including slow freezing and vitrification of colonies in suspension, are plagued by poor viability and high differentiation rates upon recovery. To facilitate research studies and clinical applications of HES cells, we have developed a cryopreservation technique based on stabilizing HES colonies adherent to or embedded in a Matrigel matrix. This method increases cell viability by over an order of magnitude compared with cryopreservation in suspension and reduces differentiation. Loading adherent HES cells with the disaccharide trehalose prior to cryopreserving in a dimethylsulfoxide-containing cryoprotectant solution further improves cell viability under certain conditions. Our proposed approach has the potential to reduce the time required to amplify frozen stocks of HES cells, minimize risk of clonal selection during freeze-thaw cycles, and facilitate storage of HES cell clone libraries.

Biocompatible Materials↗
PubMed2004

Use of protein-acrylamide copolymer hydrogels for measuring protein concentration and activity.

We report the development and characterization of a polyacrylamide-based protein immobilization strategy for surface-bound protein assays, including concentration detection, binding affinity, and enzyme kinetics. Glutathione S-transferase (GST) fusion proteins have been labeled with an acrylic moiety and attached to acrylic-functionalized glass surfaces through copolymerization with acrylic monomer. The specific attachment of GST-green fluorescent protein (GFP) fusion protein was more than sevenfold greater than the nonspecific attachment of nonacrylic-labeled GST-GFP; 0.32 ng/mm(2) of surface-attached GST-GFP was detectable by direct measurement of GFP fluorescence and this lower detection limit was reduced to 0.080 ng/mm(2) using indirect antibody-based detection. The polyacrylamide-based surface attachment strategy was also used to measure the kinetics of substrate phosphorylation by the kinase c-Src. Michaelis-Menten kinetic constants for the reaction occurring in solution were K(m) = 2.7 +/- 1.0 microM and V(max) = 8.1 +/- 3.1 (arbitrary units). Kinetic values for the reaction utilizing surface-immobilized substrate were K(m) = 0.36 +/- 0.033 microM and V(max) = 9.7 +/- 0.63 and were found to be independent of the acrylamide concentration within the copolymer. Such a surface attachment strategy should be applicable to the proteomics field and addresses denaturation and dehydration problems associated with protein microarray development.

Acrylic Resins↗
PubMed2004

Effect of sugar-phosphate mixtures on the stability of DPPC membranes in dehydrated systems.

The stabilizing role of sugars on dehydrated membranes is well established. The formation of a glassy matrix and the direct interaction between the sugars and the lipids are some of the mechanisms proposed to be involved in this stabilizing effect. Phospholipidic systems have been studied extensively as models for biological membranes and also due to the practical applications of liposomes as vehicles for drug delivery. In this work, we evaluate the effect of sugar-phosphate mixtures on the transition temperature of dehydrated 1,2-dipalmitoylphosphatidylcholine, and also examine some physical characteristics of these mixtures, such as the glass transition temperature and water sorption properties. The addition of phosphate salts to sugar systems has several interesting features that merit its consideration in formulations to protect dehydrated labile biomaterials. In particular, sucrose-phosphate mixtures provide an interesting alternative to pure saccharide formulations due to their high glass transition temperatures and their increased ability to maintain a low melting transition temperature in the presence of small amounts of water.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2004

Effect of pH, counter ion, and phosphate concentration on the glass transition temperature of freeze-dried sugar-phosphate mixtures.

PURPOSE: The aim of the present work is to study the interaction of phosphate salts with trehalose and sucrose in freeze-dried matrices, particularly the effect of the salts on the glass transition temperature (Tg) of the sugars. METHODS: Freeze-dried trehalose and sucrose systems containing different amounts of sodium or potassium phosphate were analyzed by differential scanning calorimetry to determine the Tg and by Fourier-transform infrared spectroscopy (FTIR) analysis to evaluate the strength of the interaction between sugars and phosphate ions. RESULTS: Sucrose-phosphate mixtures show an increase in Tg up to 40 degrees C in a broad pH range (4-9) compared to that of pure sucrose. Sucrose-phosphate mixtures exhibit a higher Tg than pure sucrose while retaining higher water contents. Trehalose-phosphate mixtures (having a Tg of 135 degrees C at a pH of 8.8) are a better option than pure trehalose for preservation of labile materials. The -OH stretching of the sugars in the presence of phosphates decreases with increase in pH, indicating an increase in the sugar-phosphate interaction. CONCLUSIONS: Sugar-phosphate mixtures exhibit several interesting features that make them useful for lyophilization of labile molecules; Tg values much higher than those observed for the pure sugars can be obtained upon the addition of phosphate.

Calorimetry, Differential Scanning↗
PubMed2004

Saccharomyces cerevisiae JEN1 promoter activity is inversely related to concentration of repressing sugar.

When carbon sources are changed, Saccharomyces cerevisiae transcriptional patterns drastically change. To identify genes whose transcription can be used to quantitatively measure sugar concentrations, we searched genomic expression databases for a set of genes that are highly induced during the diauxic shift, and we used the promoters from these genes to drive expression of green fluorescent protein (GFP). Certain sugars, including glucose, fructose, and mannose, repress the promoter of JEN1, which encodes a lactate-pyruvate transporter, in a dose-dependent manner. Nonrepressing carbon sources include galactose, raffinose, ethanol, lactate, and glycerol. JEN1 promoter activity is a linear function of glucose concentration when organisms are grown at a steady-state glucose concentration below 1 g/liter. JEN1 promoter repression is specific to carbon source; heat or cold shock, osmotic stress, DNA damage, and nitrogen starvation do not significantly affect promoter activity. Activation of the JEN1 promoter requires the Snf1 protein kinase, but multiple regulatory elements most likely combine to provide the linear relationship between JEN1 promoter activity and sugar concentration. Thus, a JEN1 promoter-reporter system appears to provide a good living cell biosensor for the concentration of certain sugars. The JEN1 promoter also permits quantitative regulation of cellular functions not normally controlled by sugar concentrations. For example, a strain expressing FLO1 under control of the JEN1 promoter flocculates at a low glucose concentration.

Bacterial Proteins↗
PubMed2003

EAP1, a Candida albicans gene involved in binding human epithelial cells.

Candida albicans adhesion to host tissues contributes to its virulence and adhesion to medical devices permits biofilm formation, but we know relatively little about the molecular mechanisms governing C. albicans adhesion to materials or mammalian cells. Saccharomyces cerevisiae provides an attractive model system for studying adhesion in yeast because of its well-characterized genetics and gene expression systems and the conservation of signal transduction pathways among the yeasts. In this study, we used a parallel plate flow chamber to screen and characterize attachment of a flo8Delta S. cerevisiae strain expressing a C. albicans genomic library to a polystyrene surface. The gene EAP1 was isolated as a putative cell wall adhesin. Sequence analysis of EAP1 shows that it contains a signal peptide, a glycosylphosphatidylinositol anchor site, and possesses homology to many other yeast genes encoding cell wall proteins. In addition to increasing adhesion to polystyrene, heterologous expression of EAP1 in S. cerevisiae and autonomous expression of EAP1 in a C. albicans efg1 homozygous null mutant significantly enhanced attachment to HEK293 kidney epithelial cells. EAP1 expression also restored invasive growth to haploid flo8Delta and flo11Delta strains as well as filamentous growth to diploid flo8/flo8 and flo11/flo11 strains. Transcription of EAP1 in C. albicans is regulated by the transcription factor Efg1p, suggesting that EAP1 expression is activated by the cyclic AMP-dependent protein kinase pathway.

Amino Acid Motifs↗
PubMed2002

Depression of Saccharomyces cerevisiae invasive growth on non-glucose carbon sources requires the Snf1 kinase.

Haploid Saccharomyces cerevisiae cells growing on media lacking glucose but containing high concentrations of carbon sources such as fructose, galactose, raffinose, and ethanol exhibit enhanced agar invasion. These carbon sources also promote diploid filamentous growth in response to nitrogen starvation. The enhanced invasive and filamentous growth phenotypes are suppressed by the addition of glucose to the media and require the Snf1 kinase. Mutations in the PGI1 and GND1 genes encoding carbon source utilization enzymes confer enhanced invasive growth that is unaffected by glucose but requires active Snf1. Carbon source does not modulate FLO11 flocculin expression, but enhanced polarized bud site selection is necessary for invasion on certain carbon sources. Interestingly, deletion of SNF1 blocks invasion without affecting bud site selection. Snf1 is also required for formation of spokes and hubs in multicellular mats. To examine glucose repression of invasive growth more broadly, we performed genome-wide microarray expression analysis in wild-type cells growing on glucose and galactose, and snf1 Delta cells on galactose. SNF1 probably mediates glucose repression of multiple genes potentially involved in invasive and filamentous growth. FLO11-independent cell-cell attachment, cell wall integrity, and/or polarized growth are affected by carbon source metabolism. In addition, derepression of cell cycle genes and signalling via the cAMP-PKA pathway appears to depend upon SNF1 activity during growth on galactose.

Carbon↗
PubMedDate not supplied

Protein-acrylamide copolymer hydrogels for array-based detection of tyrosine kinase activity from cell lysates.

We describe the development of an array-based assay for the molecular level detection of tyrosine kinase activity directly from cellular extracts. Glutathione S-transferase-Crkl (GST-Crkl) fusion proteins are covalently immobilized into polyacrylamide gel pads via copolymerization of acrylic monomer and acrylic-functionalized GST-Crkl protein constructs on a polyacrylamide surface. The resulting hydrogels resist nonspecific protein adsorption, permitting quantitative and reproducible determination of Abl tyrosine kinase activity and inhibition, even in the presence of a complex cell lysate mixture. Half-maximal inhibition (IC50) values for imatinib mesylate inhibition of GST-Crkl (SH3) phosphorylation by v-Abl in a purified system and Bcr-Abl within a K562 cell lysate were determined to be 1.5 and 20 microM, respectively. Additionally, the protein-acrylamide copolymer arrays detected CML cell levels as low as 15% in a background of Bcr-Abl- leukemic cells and provided the framework for the parallel evaluation of six tyrosine kinase inhibitors. Such a system may have direct application to the detection and treatment of cancers resulting from upregulated tyrosine kinase activity, such as chronic myeloid leukemia (CML). These findings also establish a basis for screening tyrosine kinase inhibitors and provide a framework on which protein-protein interactions in other complex systems can be studied.

Acrylamides↗