Predominantly Orphan Secretome in the Lung Pathogen Mycobacterium abscessus Revealed by a Multipronged Growth-Phase-Driven Strategy

The emerging lung pathogen Mycobacterium abscessus is understudied for its virulence determinants and molecular targets for diagnosis and therapeutics. Here, we report a comprehensive secretome (600 proteins) of this species, which was identified using a multipronged strategy based on genetic/genomic, proteomic, and bioinformatic approaches. In-solution digested bottom-up proteomics from various growth phases identified a total of 517 proteins, while 2D-GE proteomics identified 33 proteins. A reporter-gene-fusion-based genomic library that was custom-generated in this study enabled the detection of 23 secretory proteins. A genome-wide survey for N-terminal signal sequences using bioinformatic tools (Psortb 2.0 and SignalP 3.0) combined with a strategy of the subtraction of lipoproteins and proteins containing multiple transmembrane domains yielded 116 secretory proteins. A homology search against the M. tuberculosis database identified nine additional secretory protein homologs that lacked a secretory signal sequence. Considering the little overlap (80 proteins) among the different approaches used, this study emphasized the importance of using a multipronged strategy for a comprehensive understanding of the secretome. Notably, the majority of the secreted proteins identified (over 50%) turned out to be "orphans" (those with no known functional homologs). The revelation of these species-specific orphan proteins offers a hitherto unexplored repertoire of potential targets for diagnostic, therapeutic, and vaccine research in this emerging lung pathogen.

Structural and functional fine mapping of cysteines in mammalian glutaredoxin reveal their differential oxidation susceptibility

Protein-S-glutathionylation is a post-translational modification involving the conjugation of glutathione to protein thiols, which can modulate the activity and structure of key cellular proteins. Glutaredoxins (GLRX) are oxidoreductases that regulate this process by performing deglutathionylation. However, GLRX has five cysteines that are potentially vulnerable to oxidative modification, which is associated with GLRX aggregation and loss of activity. To date, GLRX cysteines that are oxidatively modified and their relative susceptibilities remain unknown. We utilized molecular modeling approaches, activity assays using recombinant GLRX, coupled with site-directed mutagenesis of each cysteine both individually and in combination to address the oxidizibility of GLRX cysteines. These approaches reveal that C8 and C83 are targets for S-glutathionylation and oxidation by hydrogen peroxide in vitro. In silico modeling and experimental validation confirm a prominent role of C8 for dimer formation and aggregation. Lastly, combinatorial mutation of C8, C26, and C83 results in increased activity of GLRX and resistance to oxidative inactivation and aggregation. Results from these integrated computational and experimental studies provide insights into the relative oxidizability of GLRX's cysteines and have implications for the use of GLRX as a therapeutic in settings of dysregulated protein glutathionylation.

Mitoquinone mesylate attenuates pathological features of lean and obese allergic asthma in mice

Obesity is associated with severe, difficult-to-control asthma, and increased airway oxidative stress. Mitochondrial reactive oxygen species (mROS) are an important source of oxidative stress in asthma, leading us to hypothesize that targeting mROS in obese allergic asthma might be an effective treatment. Using a mouse model of house dust mite (HDM)-induced allergic airway disease in mice fed a low- (LFD) or high-fat diet (HFD), and the mitochondrial antioxidant MitoQuinone (MitoQ), we investigated the effects of obesity and ROS on HDM-induced airway inflammation, remodeling, and airway hyperresponsiveness (AHR). Obese allergic mice showed increased lung tissue eotaxin, airway tissue eosinophilia, and AHR compared with lean allergic mice. MitoQ reduced airway inflammation, remodeling, and hyperreactivity in both lean and obese allergic mice, and tissue eosinophilia in obese-allergic mice. Similar effects were observed with decyl triphosphonium (dTPP+), the hydrophobic cationic moiety of MitoQ lacking ubiquinone. HDM-induced oxidative sulfenylation of proteins was increased particularly in HFD mice. Although only MitoQ reduced sulfenylation of proteins involved in protein folding in the endoplasmic reticulum (ER), ER stress was attenuated by both MitoQ and dTPP+ suggesting the anti-allergic effects of MitoQ are mediated in part by effects of its hydrophobic dTPP+ moiety reducing ER stress. In summary, oxidative signaling is an important mediator of allergic airway disease. MitoQ, likely through reducing protein oxidation and affecting the UPR pathway, might be effective for the treatment of asthma and specific features of obese asthma.

Glutathionylation chemistry promotes interleukin-1 beta-mediated glycolytic reprogramming and pro-inflammatory signaling in lung epithelial cells

Glycolysis is a well-known process by which metabolically active cells, such as tumor or immune cells meet their high metabolic demands. Previously, our laboratory has demonstrated that in airway epithelial cells, the pleiotropic cytokine, interleukin-1 beta (IL1B) induces glycolysis and that this contributes to allergic airway inflammation and remodeling. Activation of glycolysis is known to increase NADPH reducing equivalents generated from the pentose phosphate pathway, linking metabolic reprogramming with redox homeostasis. In addition, numerous glycolytic enzymes are known to be redox regulated. However, whether and how redox chemistry regulates metabolic reprogramming more generally remains unclear. In this study, we employed a multi-omics approach in primary mouse airway basal cells to evaluate the role of protein redox biochemistry, specifically protein glutathionylation, in mediating metabolic reprogramming. Our findings demonstrate that IL1B induces glutathionylation of multiple proteins involved in metabolic regulation, notably in the glycolysis pathway. Cells lacking Glutaredoxin-1 (Glrx), the enzyme responsible for reversing glutathionylation, show modulation of multiple metabolic pathways including an enhanced IL1B-induced glycolytic response. This was accompanied by increased secretion of thymic stromal lymphopoietin (TSLP), a cytokine important in asthma pathogenesis. Targeted inhibition of glycolysis prevented TSLP release, confirming the functional relevance of enhanced glycolysis in cells stimulated with IL1B. Collectively, data herein point to an intriguing link between glutathionylation chemistry and glycolytic reprogramming in epithelial cells and suggest that glutathionylation chemistry may represent a therapeutic target in pulmonary pathologies with perturbations in the glycolysis pathway.

Ciliary Ca2+ pumps regulate intraciliary Ca2+ from the action potential and may co-localize with ciliary voltage-gated Ca2+ channels

Calcium ions (Ca2+) entering cilia through the ciliary voltage-gated calcium channels (CaV) during the action potential causes reversal of the ciliary power stroke and backward swimming in Paramecium tetraurelia. How calcium is returned to the resting level is not yet clear. Our focus is on calcium pumps as a possible mechanism. There are 23 P. tetraurelia genes for calcium pumps that are members of the family of plasma membrane Ca2+ ATPases (PMCAs). They have domains homologous to those found in mammalian PMCAs. Of the 13 pump proteins previously identified in cilia, ptPMCA2a and ptPMCA2b are most abundant in the cilia. We used RNAi to examine which PMCA might be involved in regulating intraciliary Ca2+ after the action potential. RNAi for only ptPMCA2a and ptPMCA2b causes cells to significantly prolong their backward swimming, which indicates that Ca2+ extrusion in the cilia is impaired when these PMCAs are depleted. We used immunoprecipitations (IP) to find that ptPMCA2a and ptPMCA2b are co-immunoprecipitated with the CaV channel α1 subunits that are found only in the cilia. We used iodixanol (OptiPrep) density gradients to show that ptPMCA2a and ptPMCA2b and CaV1c are found in the same density fractions. These results suggest that ptPMCA2a and ptPMCA2b are located in the proximity of ciliary CaV channels.

Coactosin Phosphorylation Controls Entamoeba histolytica Cell Membrane Protrusions and Cell Motility

Invasion of the colon wall by Entamoeba histolytica during amoebic dysentery entails migration of trophozoites through tissue layers that are rich in extracellular matrix. Transcriptional silencing of the E. histolytica surface metalloprotease EhMSP-1 produces hyperadherent less-motile trophozoites that are deficient in forming invadosomes. Reversible protein phosphorylation is often implicated in regulation of cell motility and invadosome formation. To identify such intermediaries of the EhMSP-1-silenced phenotype, here we compared the phosphoproteomes of EhMSP-1-silenced and vector control trophozoites by using quantitative tandem mass spectrometry-based proteomics. Six proteins were found to be differentially phosphorylated in EhMSP-1-silenced and control cells, including EhCoactosin, a member of the ADF/cofilin family of actin-binding proteins, which was more frequently phosphorylated at serine 147. Regulated overexpression of wild-type, phosphomimetic, and nonphosphorylatable EhCoactosin variants was used to test if phosphorylation functions in control of E. histolytica actin dynamics. Each of the overexpressed proteins colocalized with F-actin during E. histolytica phagocytosis. Nonetheless, trophozoites overexpressing an EhCoactosin phosphomimetic mutant formed more and poorly coordinated cell membrane protrusions compared to those in control or cells expressing a nonphosphorylatable mutant, while trophozoites overexpressing nonphosphorylatable EhCoactosin were significantly more motile within a model of mammalian extracellular matrix. Therefore, although EhCoactosin's actin-binding ability appeared unaffected by phosphorylation, EhCoactosin phosphorylation helps to regulate amoebic motility. These data help to understand the mechanisms underlying altered adherence and motility in EhMSP-1-silenced trophozoites and lay the groundwork for identifying kinases and phosphatases critical for control of amoebic invasiveness.IMPORTANCE Invasive amoebiasis, caused by the intestinal parasite Entamoeba histolytica, causes life-threatening diarrhea and liver abscesses, but, for unknown reasons, only approximately 10% of E. histolytica infections become symptomatic. A key requirement of invasion is the ability of the parasite to migrate through tissue layers. Here, we systematically looked for differences in protein phosphorylation between control parasites and a previously identified hyperadherent E. histolytica cell line that has reduced motility. We identified EhCoactosin, an actin-binding protein not previously known to be phosphoregulated, as one of the differentially phosphorylated proteins in E. histolytica and demonstrated that EhCoactosin phosphorylation functions in control of cell membrane dynamics and amoebic motility. This and the additional differentially phosphorylated proteins reported lay the groundwork for identifying kinases and phosphatases that regulate tissue invasiveness.

Dysregulation of the glutaredoxin/S-glutathionylation redox axis in lung diseases

Glutathione is a major redox buffer, reaching millimolar concentrations within cells and high micromolar concentrations in airways. While glutathione has been traditionally known as an antioxidant defense mechanism that protects the lung tissue from oxidative stress, glutathione more recently has become recognized for its ability to become covalently conjugated to reactive cysteines within proteins, a modification known as S-glutathionylation (or S-glutathiolation or protein mixed disulfide). S-glutathionylation has the potential to change the structure and function of the target protein, owing to its size (the addition of three amino acids) and charge (glutamic acid). S-glutathionylation also protects proteins from irreversible oxidation, allowing them to be enzymatically regenerated. Numerous enzymes have been identified to catalyze the glutathionylation/deglutathionylation reactions, including glutathione S-transferases and glutaredoxins. Although protein S-glutathionylation has been implicated in numerous biological processes, S-glutathionylated proteomes have largely remained unknown. In this paper, we focus on the pathways that regulate GSH homeostasis, S-glutathionylated proteins, and glutaredoxins, and we review methods required toward identification of glutathionylated proteomes. Finally, we present the latest findings on the role of glutathionylation/glutaredoxins in various lung diseases: idiopathic pulmonary fibrosis, asthma, and chronic obstructive pulmonary disease.

Direct cysteine sulfenylation drives activation of the Src kinase

The Src kinase controls aspects of cell biology and its activity is regulated by intramolecular structural changes induced by protein interactions and tyrosine phosphorylation. Recent studies indicate that Src is additionally regulated by redox-dependent mechanisms, involving oxidative modification(s) of cysteines within the Src protein, although the nature and molecular-level impact of Src cysteine oxidation are unknown. Using a combination of biochemical and cell-based studies, we establish the critical importance of two Src cysteine residues, Cys-185 and Cys-277, as targets for H2O2-mediated sulfenylation (Cys-SOH) in redox-dependent kinase activation in response to NADPH oxidase-dependent signaling. Molecular dynamics and metadynamics simulations reveal the structural impact of sulfenylation of these cysteines, indicating that Cys-277-SOH enables solvent exposure of Tyr-416 to promote its (auto)phosphorylation, and that Cys-185-SOH destabilizes pTyr-527 binding to the SH2 domain. These redox-dependent Src activation mechanisms offer opportunities for development of Src-selective inhibitors in treatment of diseases where Src is aberrantly activated.

Bacterial Lipoproteins Constitute the TLR2-Stimulating Activity of Serum Amyloid A

Studies comparing endogenous and recombinant serum amyloid A (SAA) have generated conflicting data on the proinflammatory function of these proteins. In exploring this discrepancy, we found that in contrast to commercially sourced recombinant human SAA1 (hSAA1) proteins produced in Escherichia coli, hSAA1 produced from eukaryotic cells did not promote proinflammatory cytokine production from human or mouse cells, induce Th17 differentiation, or stimulate TLR2. Proteomic analysis of E. coli-derived hSAA1 revealed the presence of numerous bacterial proteins, with several being reported or probable lipoproteins. Treatment of hSAA1 with lipoprotein lipase or addition of a lipopeptide to eukaryotic cell-derived hSAA1 inhibited or induced the production of TNF-α from macrophages, respectively. Our results suggest that a function of SAA is in the binding of TLR2-stimulating bacterial proteins, including lipoproteins, and demand that future studies of SAA employ a recombinant protein derived from eukaryotic cells.

Avian lungs: A novel scaffold for lung bioengineering

Allogeneic lung transplant is limited both by the shortage of available donor lungs and by the lack of suitable long-term lung assist devices to bridge patients to lung transplantation. Avian lungs have different structure and mechanics resulting in more efficient gas exchange than mammalian lungs. Decellularized avian lungs, recellularized with human lung cells, could therefore provide a powerful novel gas exchange unit for potential use in pulmonary therapeutics. To initially assess this in both small and large avian lung models, chicken (Gallus gallus domesticus) and emu (Dromaius novaehollandiae) lungs were decellularized using modifications of a detergent-based protocol, previously utilized with mammalian lungs. Light and electron microscopy, vascular and airway resistance, quantitation and gel analyses of residual DNA, and immunohistochemical and mass spectrometric analyses of remaining extracellular matrix (ECM) proteins demonstrated maintenance of lung structure, minimal residual DNA, and retention of major ECM proteins in the decellularized scaffolds. Seeding with human bronchial epithelial cells, human pulmonary vascular endothelial cells, human mesenchymal stromal cells, and human lung fibroblasts demonstrated initial cell attachment on decellularized avian lungs and growth over a 7-day period. These initial studies demonstrate that decellularized avian lungs may be a feasible approach for generating functional lung tissue for clinical therapeutics.

TGF-β1-induced deposition of provisional extracellular matrix by tracheal basal cells promotes epithelial-to-mesenchymal transition in a c-Jun NH2-terminal kinase-1-dependent manner

Epithelial cells have been suggested as potential drivers of lung fibrosis, although the epithelial-dependent pathways that promote fibrogenesis remain unknown. Extracellular matrix is increasingly recognized as an environment that can drive cellular responses in various pulmonary diseases. In this study, we demonstrate that transforming growth factor-β1 (TGF-β1)-stimulated mouse tracheal basal (MTB) cells produce provisional matrix proteins in vitro, which initiate mesenchymal changes in subsequently freshly plated MTB cells via Rho kinase- and c-Jun NH2-terminal kinase (JNK1)-dependent processes. Repopulation of decellularized lung scaffolds, derived from mice with bleomycin-induced fibrosis or from patients with idiopathic pulmonary fibrosis, with wild-type MTB cells resulted in a loss of epithelial gene expression and augmentation of mesenchymal gene expression compared with cells seeded into decellularized normal lungs. In contrast, Jnk1-/- basal cells seeded into fibrotic lung scaffolds retained a robust epithelial expression profile, failed to induce mesenchymal genes, and differentiated into club cell secretory protein-expressing cells. This new paradigm wherein TGF-β1-induced extracellular matrix derived from MTB cells activates a JNK1-dependent mesenchymal program, which impedes subsequent normal epithelial cell homeostasis, provides a plausible scenario of chronic aberrant epithelial repair, thought to be critical in lung fibrogenesis. This study identifies JNK1 as a possible target for inhibition in settings wherein reepithelialization is desired.

Mouse serum exosomal proteomic signature in response to asbestos exposure

Asbestos-induced diseases like fibrosis and mesothelioma are very aggressive, without any treatment options. These diseases are diagnosed only at the terminal stages due to lack of early stage biomarkers. The recent discovery of exosomes as circulating biomarkers led us to look for exosomal biomarkers of asbestos exposure in mouse blood. In our model, mice were exposed to asbestos as a single bolus dose by oropharyngeal aspiration. Fifty-six days later blood was collected, exosomes were isolated from plasma and characterized and subjected to proteomic analysis using Tandem Mass Tag labeling. We identified many proteins, some of which were more abundant in asbestos exposed mouse serum exosomes, and three selected proteins were validated by immunoblotting. Our study is the first to show that serum exosomal proteomic signatures can reveal some important proteins relevant to asbestos exposure that have the potential to be validated as candidate biomarkers. We hope to extrapolate the positive findings of this study to humans in future studies.

Exosomes from asbestos-exposed cells modulate gene expression in mesothelial cells

Asbestos exposure is a determinate cause of many diseases, such as mesothelioma, fibrosis, and lung cancer, and poses a major human health hazard. At this time, there are no identified biomarkers to demarcate asbestos exposure before the presentation of disease and symptoms, and there is only limited understanding of the underlying biology that governs asbestos-induced disease. In our study, we used exosomes, 30-140 nm extracellular vesicles, to gain insight into these knowledge gaps. As inhaled asbestos is first encountered by lung epithelial cells and macrophages, we hypothesize that asbestos-exposed cells secrete exosomes with signature proteomic cargo that can alter the gene expression of mesothelial cells, contributing to disease outcomes like mesothelioma. In the present study using lung epithelial cells (BEAS2B) and macrophages (THP-1), we first show that asbestos exposure causes changes in abundance of some proteins in the exosomes secreted from these cells. Furthermore, exposure of human mesothelial cells (HPM3) to these exosomes resulted in gene expression changes related to epithelial-to-mesenchymal transition and other cancer-related genes. This is the first report to indicate that asbestos-exposed cells secrete exosomes with differentially abundant proteins and that those exosomes have a gene-altering effect on mesothelial cells.-Munson, P., Lam, Y.-W., Dragon, J. MacPherson, M., Shukla, A. Exosomes from asbestos-exposed cells modulate gene expression in mesothelial cells.

Salt Response Analysis in Two Rice Cultivars at Seedling Stage

In order to explore the salt-stress responses of two rice varieties, the physiological responses and biochemical responses were investigated using proteomics and classical biochemical methods. The results showed that the seedling growth was inhibited under salt condition in two rice varieties, the seedling growth in the tolerant variety was better than the sensitive variety. The sensitive variety(L7) appeared obvious salt-injury under 3-day salt stress, the tolerant variety (T07339) keep normal growth under 7-day salt stress except that the shoot length was decreased. Through the growth-parameters analysis, most of them in L7 were restrained by salinity and most in T07339 were unaffected. In T07339, the fresh root weight, the content of chlorophyll and the fresh shoot weight were even increased after 7 days of salt stress. A comparison of two-dimensional gel electrophoresis (2-DGE) protein profiles revealed 8 differently expressed proteins. Four proteins were expressed in different pattern between sensitive and tolerant varieties. These results provide novel insights into the investigations of the salt-response proteins that involved in improved salt tolerance.

Exploration of the bovine colostrum proteome and effects of heat treatment time on colostrum protein profile

Heat treatment of colostrum is performed on modern dairy farms to reduce pathogenic contamination before hand-feeding the colostrum to newborn calves; however, limited data are available concerning effects of heat treatment on biologically active proteins in colostrum. The objective of this exploratory study was to investigate effects of heat treatment and length of heat treatment on colostrum protein profile. Colostrum samples were collected from Holstein cows within 12 h after parturition and assigned to the following groups: heat treatment at 60°C for 0 (untreated control), 30, 60, or 90 min. Samples were fractionated using acid precipitation, followed by ultracentrifugation and ProteoMiner (Bio-Rad Laboratories, Hercules, CA) treatment, and tandem-mass tagging was used to comparatively assess the low abundance protein profile. A total of 162 proteins were identified with more than 2 peptides in the low abundance protein enriched fraction. Of these, 62 differed in abundance by more than 2-fold in heat treated samples compared with the unheated control. The majority of proteins affected by heat treatment were involved in immunity, enzyme function, and transport-related processes; affected proteins included lactadherin, chitinase-3-like protein 1, and complement component C9. These results provide a foundation for further research to determine optimum heat treatment practices to ensure newborn calves are fed colostrum-containing proteins with the highest nutritional and biological value.

The lysosomal protein cathepsin L is a progranulin protease

Haploinsufficiency of GRN, the gene encoding progranulin (PGRN), causes frontotemporal lobar degeneration (FTLD), the second most common cause of early-onset dementia. Receptor-mediated lysosomal targeting has been shown to regulate brain PGRN levels, and complete deficiency of PGRN is a direct cause of neuronal ceroid lipofuscinosis (NCL), a lysosomal storage disease. Here we show that the lysosomal cysteine protease cathepsin L (Cat L) can mediate the proteolytic cleavage of intracellular PGRN into poly-granulin and granulin fragments. Further, PGRN and Cat L co-localize in lysosomes of HEK293 cells, iPSC-derived neurons and human cortical neurons from human postmortem tissue. These data identify Cat L as a key intracellular lysosomal PGRN protease, and provides an intriguing new link between lysosomal dysfunction and FTLD.

Scaling Proteome-Wide Reactions of Activity-Based Probes

Unified analysis of complex reactions of an activity-based probe with proteins in a proteome remains an unsolved challenge. We propose a power expression, rate = k^obs[Probe]^α, for scaling the progress of proteome-wide reactions and use the scaling factor (0 ≤ α ≤ 1) as an apparent, partial order with respect to the probe to measure the "enzyme-likeness" for a protein in reaction acceleration. Thus, α reports the intrinsic reactivity of the protein with the probe. When α = 0, the involved protein expedites the reaction to the maximal degree; when α = 1, the protein reacts with the probe via an unaccelerated, bimolecular reaction. The selectivity (β) of the probe reacting with two proteins is calculated as a ratio of conversion factors (k^obs values) for corresponding power equations. A combination of α and β provides a tiered system for quantitatively assessing the probe efficacy; an ideal probe exhibits high reactivity with its protein targets (low in α) and is highly selective (high in β) in forming the probe-protein adducts. The scaling analysis was demonstrated using proteome-wide reactions of HT-29 cell lysates with a model probe of threonine β-lactone.

Development and Applications of a Calmodulin-Based Fusion Protein System for the Expression and Purification of WW and Zinc Finger Modules

Calmodulin from Homo sapiens is an α-helical calcium-binding protein that expresses to high levels in E. coli. When the N-terminus of a calmodulin variant is bound to Ca²⁺, it undergoes a conformational change, exposing hydrophobic pockets. This property can be utilized for purification purposes, as these pockets bind to phenyl sepharose resin with high affinity. Washing with EDTA chelates the Ca²⁺ ions from the protein, inducing a conformational change back to the more folded state and eluting the protein from the column. We describe herein the use of a protein expression and purification technique using the calmodulin variant and a short linker for proteolytic cleavage by the mutant NIa-Pro tobacco etch virus protease. We have shown this approach to be useful in obtaining purified quantities of various small proteins that could not be expressed using other methods, including high enough concentrations of a designed WW domain protein for NMR structural analysis. We have also obtained promising results on the usefulness of this procedure to express and purify zinc finger proteins without the addition of zinc ions or other cofactors.

Comparative Decellularization and Recellularization of Wild-Type and Alpha 1,3 Galactosyltransferase Knockout Pig Lungs: A Model for Ex Vivo Xenogeneic Lung Bioengineering and Transplantation

BACKGROUND

A novel potential approach for lung transplantation could be to utilize xenogeneic decellularized pig lung scaffolds that are recellularized with human lung cells. However, pig tissues express several immunogenic proteins, notably galactosylated cell surface glycoproteins resulting from alpha 1,3 galactosyltransferase (α-gal) activity, that could conceivably prevent effective use. Use of lungs from α-gal knock out (α-gal KO) pigs presents a potential alternative and thus comparative de- and recellularization of wild-type and α-gal KO pig lungs was assessed.

METHODS

Decellularized lungs were compared by histologic, immunohistochemical, and mass spectrometric techniques. Recellularization was assessed following compartmental inoculation of human lung bronchial epithelial cells, human lung fibroblasts, human bone marrow-derived mesenchymal stromal cells (all via airway inoculation), and human pulmonary vascular endothelial cells (CBF) (vascular inoculation).

RESULTS

No obvious differences in histologic structure was observed but an approximate 25% difference in retention of residual proteins was determined between decellularized wild-type and α-gal KO pig lungs, including retention of α-galactosylated epitopes in acellular wild-type pig lungs. However, robust initial recellularization and subsequent growth and proliferation was observed for all cell types with no obvious differences between cells seeded into wild-type versus α-gal KO lungs.

CONCLUSION

These proof of concept studies demonstrate that decellularized wild-type and α-gal KO pig lungs can be comparably decellularized and comparably support initial growth of human lung cells, despite some differences in retained proteins. α-Gal KO pig lungs are a suitable platform for further studies of xenogeneic lung regeneration.

Characterization of the bovine milk proteome in early-lactation Holstein and Jersey breeds of dairy cows

Milk is a highly nutritious natural product that provides not only a rich source of amino acids to the consumer but also hundreds of bioactive peptides and proteins known to elicit health-benefitting activities. We investigated the milk protein profile produced by Holstein and Jersey dairy cows maintained under the same diet, management and environmental conditions using proteomic approaches that optimize protein extraction and characterization of the low abundance proteins within the skim milk fraction of bovine milk. In total, 935 low abundance proteins were identified. Gene ontology classified all proteins identified into various cellular localization and function categories. A total of 43 low abundance proteins were differentially expressed between the two dairy breeds. Bioactive proteins involved in host-defense, including lactotransferrin (P=0.0026) and complement C2 protein (P=0.0001), were differentially expressed by the two breeds, whereas others such as osteopontin (P=0.1788) and lactoperoxidase (P=0.2973) were not. This work is the first to outline the protein profile produced by two important breeds of dairy cattle maintained under the same diet, environment and management conditions in order to observe likely true breed differences. This research now allows us to better understand and contrast further research examining the bovine proteome that includes these different breeds.

BIOLOGICAL SIGNIFICANCE

Within the last decade, the amount of research characterizing the bovine milk proteome has increased due to growing interest in the bioactive proteins that are present in milk. Proteomic analysis of low abundance whey proteins has mainly focused on human breast milk; however, previous research has highlighted the presence of bioactive proteins in bovine milk. Recent publications outlining the cross-reactivity of bovine bioactive proteins on human biological function highlight the need for further investigation into the bovine milk proteome. The rationale behind this study is to characterize and compare the low abundance protein profile in the skim milk fraction produced from Holstein and Jersey breeds of dairy cattle, which are two major dairy cattle breeds in the USA. A combination of fractionation strategies was used to efficiently enrich the low abundance proteins from bovine skim milk for proteomic profiling. A total of 935 low abundance proteins were identified and compared between the two bovine breeds. The results from this study provide insight into breed differences and similarities in the milk proteome profile produced by two breeds of dairy cattle.

Alteration in abundance of specific membrane proteins of Aggregatibacter actinomycetemcomitans is attributed to deletion of the inner membrane protein MorC

Aggregatibacter actinomycetemcomitans is an important pathogen in the etiology of human periodontal and systemic diseases. Inactivation of the gene coding for the inner membrane protein, morphogenesis protein C (MorC), results in pleotropic effects pertaining to the membrane structure and function of this bacterium. The role of this protein in membrane biogenesis is unknown. To begin to understand the role of this conserved protein, stable isotope dimethyl labeling in conjunction with MS was used to quantitatively analyze differences in the membrane proteomes of the isogenic mutant and wild-type strain. A total of 613 proteins were quantified and 601 of these proteins were found to be equal in abundance between the two strains. The remaining 12 proteins were found in lesser (10) or greater (2) abundance in the membrane preparation of the mutant strain compared with the wild-type strain. The 12 proteins were ascribed functions associated with protein quality control systems, oxidative stress responses, and protein secretion. The potential relationship between these proteins and the phenotypes of the MorC mutant strain is discussed.

Control of cell migration direction by inducing cell shape asymmetry with patterned topography

In this study, we explored the concept of introducing asymmetry to cell shapes by patterned cell culture substrates, and investigated the consequence of this induced asymmetry to cell migration behaviors. Three patterns, named "Squares", "Grating", and "Arcs" were fabricated, representing different levels of rotational asymmetry. Using time-lapse imaging, we systematically compared the motility and directionality of mouse osteoblastic cells MC3T3-E1 cultured on these patterns. Cells were found to move progressively faster on "Arcs" than on "Grating", and cells on "Squares" were the slowest, suggesting that cell motility correlates with the level of rotational asymmetry of the repeating units of the pattern. Among these three patterns, on the "Arcs" pattern, the least symmetrical one, cells not only moved with the highest velocity but also the strongest directional persistence. Although this enhanced motility was not associated with the detected number of focal adhesion sites in the cells, the pattern asymmetry was reflected in the asymmetrical cell spreading. Cells on the "Arcs" pattern consistently displayed larger cytoplasmic protrusion on one side of the cell. This asymmetry in cell shape determined the direction and speed of cell migration. These observations suggest that topographical patterns that enhance the imbalance between the leading and trailing fronts of adherent cells will increase cell speed and control movement directions. Our discovery shows that complex cell behaviors such as the direction of cell movement are influenced by simple geometrical principles, which can be utilized as the design foundation for platforms that guide and sort cultured cells.

Potential-based methodology for active sound control in three dimensional settings

This paper extends a potential-based approach to active noise shielding with preservation of wanted sound in three-dimensional settings. The approach, which was described in a previous publication [Lim et al., J. Acoust. Soc. Am. 129(2), 717-725 (2011)], provides several significant advantages over conventional noise control methods. Most significantly, the methodology does not require any information including the characterization of sources, impedance boundary conditions and surrounding medium, and that the methodology automatically differentiates between the wanted and unwanted sound components. The previous publication proved the concept in one-dimensional conditions. In this paper, the approach for more realistic conditions is studied by numerical simulation and experimental validation in three-dimensional cases. The results provide a guideline to the implementation of the active shielding method with practical three-dimensional conditions. Through numerical simulation it is demonstrated that while leaving the wanted sound unchanged, the developed approach offers selective volumetric noise cancellation within a targeted domain. In addition, the method is implemented in a three-dimensional experiment with a white noise source in a semi-anechoic chamber. The experimental study identifies practical difficulties and limitations in the use of the approach for real applications.

Identification of DUOX1-dependent redox signaling through protein S-glutathionylation in airway epithelial cells

The NADPH oxidase homolog dual oxidase 1 (DUOX1) plays an important role in innate airway epithelial responses to infection or injury, but the precise molecular mechanisms are incompletely understood and the cellular redox-sensitive targets for DUOX1-derived H₂O₂ have not been identified. The aim of the present study was to survey the involvement of DUOX1 in cellular redox signaling by protein S-glutathionylation, a major mode of reversible redox signaling. Using human airway epithelial H292 cells and stable transfection with DUOX1-targeted shRNA as well as primary tracheal epithelial cells from either wild-type or DUOX1-deficient mice, DUOX1 was found to be critical in ATP-stimulated transient production of H₂O₂ and increased protein S-glutathionylation. Using cell pre-labeling with biotin-tagged GSH and analysis of avidin-purified proteins by global proteomics, 61 S-glutathionylated proteins were identified in ATP-stimulated cells compared to 19 in untreated cells. Based on a previously established role of DUOX1 in cell migration, various redox-sensitive proteins with established roles in cytoskeletal dynamics and/or cell migration were evaluated for S-glutathionylation, indicating a critical role for DUOX1 in ATP-stimulated S-glutathionylation of β-actin, peroxiredoxin 1, the non-receptor tyrosine kinase Src, and MAPK phosphatase 1. Overall, our studies demonstrate the importance of DUOX1 in epithelial redox signaling through reversible S-glutathionylation of a range of proteins, including proteins involved in cytoskeletal regulation and MAPK signaling pathways involved in cell migration.

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ATP-mediated activation of DUOX1 results in increased protein S-glutathionylation.

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ATP stimulation promotes S-glutathionylation of a number of diverse proteins.

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DUOX1-dependent S-glutathionylation affects proteins involved in cell migration.

Site-specific S-nitrosylation of integrin α6 increases the extent of prostate cancer cell migration by enhancing integrin β1 association and weakening adherence to laminin-1

The increased mortality in prostate cancer is usually the result of metastatic progression of the disease from the organ-confined location. Among the major events in this progression cascade are enhanced cell migration and loss of adhesion. Moreover, elevated levels of nitric oxide (NO) and inducible nitric oxide synthase (iNOS) found within the tumor microenvironment are hallmarks of progression of this cancer. To understand the role of nitrosative stress in prostate cancer progression, we investigated the effects of NO and iNOS on prostate cancer cell migration and adhesion. Our results indicate that ectopic expression of iNOS in prostate cancer cells increased the extent of cell migration, which could be blocked by selective ITGα6 blocking antibody or iNOS inhibitors. Furthermore, iNOS was found to cause S-nitrosylation of ITGα6 at Cys86 in prostate cancer cells. By comparing the activities of wild-type ITGα6 and a Cys86 mutant, we showed that treatment of prostate cancer cells with NO increased the level of ITGα6 heterodimerization with ITGβ1 but not with ITGβ4. Finally, S-nitrosylation of ITGα6 weakened its binding to laminin-β1 and weakened the adhesion of prostate cancer cells to laminin-1. In conclusion, S-nitrosylation of ITGα6 increased the extent of prostate cancer cell migration, which could be a potential mechanism of NO- and iNOS-induced enhancement of prostate cancer metastasis.

Phosphorylation of human estrogen receptor-beta at serine 105 inhibits breast cancer cell migration and invasion

Multiple phosphorylation sites on the human estrogen receptor (hER)α were identified and shown to influence mammary carcinogenesis. In contrast, functional phosphorylation sites of hERβ have yet to be experimentally identified and validated. Here, using mass spectrometry, we uncovered three serines (S75, S87, and S105) in the N-terminus of hERβ as targets of ERK1/2 and p38 kinases. We raised a specific antibody against phosphorylated S105 (pS105) and demonstrated that this site was endogenously phosphorylated in MDA-MB-231 and BT-474 cells. A phospho-mimetic mutant generated from hERβ1 was found to exhibit higher transactivation activity than hERβ1. Ectopic expression of this mutant inhibited cell migration and invasion, but did not affect cell growth and cell-cycle progression in these cell models. In breast cancer specimens, pS105-hERβ immunoreactivity was detected with a higher prevalence and intensity than that of hERβ1. These results underscore the functional importance of the first experimentally identified hERβ-phosphorylation site in breast cancer.

Multi-domain active sound control and noise shielding

This paper describes an active sound control methodology based on difference potentials. The main feature of this methodology is its ability to automatically preserve "wanted" sound within a domain while cancelling "unwanted" noise from outside the domain. This method of preservation of the wanted sounds by active shielding control is demonstrated with various broadband and realistic sound sources such as human voice and music in multiple domains in a one-dimensional enclosure. Unlike many other conventional active control methods, the proposed approach does not require the explicit characterization of the wanted sound to be preserved. The controls are designed based on the measurements of the total field on the boundaries of the shielded domain only, which is allowed to be multiply connected. The method is tested in a variety of experimental cases. The typical attenuation of the unwanted noise is found to be about 20 dB over a large area of the shielded domain and the original wanted sound field is preserved with errors of around 1 dB and below through a broad frequency range up to 1 kHz.

Biochemical characterization of the cell-biomaterial interface by quantitative proteomics

Surface topography and texture of cell culture substrata can affect the differentiation and growth of adherent cells. The biochemical basis of the transduction of the physical and mechanical signals to cellular responses is not well understood. The lack of a systematic characterization of cell-biomaterial interaction is the major bottleneck. This study demonstrated the use of a novel subcellular fractionation method combined with quantitative MS-based proteomics to enable the robust and high-throughput analysis of proteins at the adherence interface of Madin-Darby canine kidney cells. This method revealed the enrichment of extracellular matrix proteins and membrane and stress fibers proteins at the adherence surface, whereas it shows depletion of extracellular matrix belonging to the cytoplasmic, nucleus, and lateral and apical membranes. The asymmetric distribution of proteins between apical and adherence sides was also profiled. Apart from classical proteins with clear involvement in cell-material interactions, proteins previously not known to be involved in cell attachment were also discovered.

Changes in Serum Proteomic Patterns by Presurgical -Tocopherol and L-Selenomethionine Supplementation in Prostate Cancer

BACKGROUND

Evidence of the chemopreventive effects of the dietary antioxidants alpha-tocopherol (vitamin E) and l-selenomethionine (selenium) comes from secondary analysis of two phase III clinical trials that found treatment with these antioxidants reduced the incidence of prostate cancer. To determine the effects of selenium and vitamin E in blood and prostate tissue, we undertook a preoperative feasibility study complementary to the currently ongoing Selenium and Vitamin E Cancer Prevention Trial.

METHODS

Forty-eight patients with clinically localized prostate cancer enrolled on this 2 x 2 factorial design study were randomized to take selenium, vitamin E, both, or placebo for 3 to 6 weeks before prostatectomy. Sera were collected from patients before and after dietary supplementation. Thirty-nine patients were evaluable, and 29 age-matched disease-free men served as controls. Mass profiling of lipophilic serum proteins of lower molecular weight (2-13.5 kDa) was conducted, and mass spectra data were analyzed using custom-designed software.

RESULTS

Weighted voting analyses showed a change in sera classification from cancerous to healthy for some patients with prostate cancer after dietary intervention. ANOVA analysis showed significantly different treatment effects on prediction strength changes among the four groups at a 95% confidence level. Eliminating an outlying value and performing post hoc analysis using Fisher's least significant difference method showed that effects in the group treated with the combination were significantly different from those of the other groups.

CONCLUSION

In sera from patients with prostate cancer, selenium and vitamin E combined induced statistically significant proteomic pattern changes associated with prostate cancer-free status.

MONITORING THE SEROLOGICAL PROTEOME: THE LATEST MODALITY IN PROSTATE CANCER DETECTION

PURPOSE

Various strategies have recently emerged to improve the diagnostic prediction of prostate cancer (CaP). One such strategy includes the mass profiling of serum protein fractions selectively adsorbed onto chemically modified probes. In the current study we further validated this approach, while offering a more versatile, less expensive and yet equally predictive alternative to existing technologies.

MATERIALS AND METHODS

A solid core lipophilic C-18 resin was used to extract and enrich the low molecular weight protein fraction from patient serum for further analysis by mass spectrometry. Mass spectra generated from a 48 patient training set were data mined using multivariate analysis to identify diagnostically significant protein peaks. These peaks were then used to test a blinded study set comprising 168 patients with common statistical algorithms and commercially available software packages.

RESULTS

A total of 36 peaks generated from the training set were used to test the combined set of 168 serum samples obtained from 98 healthy individuals and 70 patients with CaP. We report a sensitivity of 94.1% and a specificity of 99.0% with 1 false-positive, 4 false-negative and 5 nondiagnosed cases.

CONCLUSIONS

Our results further indicate that mass profiling of serological proteins provides a means for the accurate detection of CaP. In addition, our approach was found to be superior to chip based protocols, generating rich, sharp, highly reproducible spectra attainable in a high throughput manner and at minimal cost. This technique is also scaleable for subsequent protein characterization using multidimensional protein identification technologies. Finally, analyses of mass spectra with commercially available statistical applications was found to be highly effective in generating highly discriminatory m/z values for CaP diagnosis.

The immunostimulatory activity and stability of grass carp (Ctenopharyngodon idellus) roe lectin

A hexameric rhamnose-specific lectin with a molecular mass of 205kDa and exhibiting some N-terminal sequence similarity to other fish lectins was isolated from roe of the grass carp (Ctenopharyngodon idellus) by affinity chromatography on rhamnose-Sepharose and ion exchange chromatography by fast protein liquid chromatography on a Mono S column. The lectin exhibited mitogenic activity toward murine splenocytes with a potency lower than that of the plant lectin ConA. It exerted a stimulatory effect at a concentration of 10 micro g/ml on the phagocytic activity of seabream (Sparus sarba) macrophages. It was unstable toward heat (temperature > or =40 degrees C), acid (0.1M HCl), alkali (0.1M NaOH), trypsin and succinylation.

Branched fatty acids in dairy and beef products markedly enhance alpha-methylacyl-CoA racemase expression in prostate cancer cells in vitro

An enzyme previously identified as alpha-methylacyl-CoA racemase (AMACR) is overexpressed in high-grade prostatic intraepithelial neoplasia and in a majority (60-100%) of prostate cancers (CaPs) as compared with normal and benign hyperplastic lesions of the prostate, where it is minimally expressed. This enzyme is required for the beta-oxidation of branched-chain fatty acids, which include phytanic acid and its alpha-oxidation product, pristanic acid. Interestingly, there is an established correlation between CaP risk and the consumption of dairy and beef products, which also contain marked quantities of these two phytols. In this context, it has also been reported that sex steroids influence lipogenesis through the induction of fatty acid synthase in CaP-derived cell lines and CaP tissues. These findings indicate a potential role for AMACR and the possible influence of sex steroids in both the early development and subsequent progression of CaP. Despite the recent interest in AMACR as a histological marker for CaP, little is known about the regulation of this enzyme and its role in CaP development. To identify potential AMACR-regulating factors, we treated LNCaP cells (an androgen-responsive CaP-derived cell line) and NPrEC cells (a normal prostate basal epithelial cell line) with increasing concentrations of pristanic acid, phytanic acid, 5alpha-dihydrotestosterone, and 17beta-estradiol. Neither the biologically potent androgen 5alpha-dihydrotestosterone nor 17beta-estradiol had any apparent effect on AMACR expression at the protein or transcriptional levels in either cell line. Conversely, pristanic acid and, to a much lesser extent, phytanic acid markedly increased AMACR protein levels selectively in the LNCaP cell line, but not the NPrEC cell line. However, no change was measured at the transcriptional level in either cell line. AMACR is therefore significantly increased at the protein level in CaP cells, through what appears to be the stabilizing effect of the same fatty acids that are present at appreciable concentrations in beef and dairy products, which have been associated with CaP risk. Our findings therefore provide a link between the consumption of dietary fatty acids and the enhanced expression of AMACR, an enzyme that may play an important role in genesis and progression of CaP.

Purification and characterization of a rhamnose-binding lectin with immunoenhancing activity from grass carp (Ctenopharyngodon idellus) ovaries

A rhamnose-specific lectin was isolated from ovaries of the grass carp (Ctenopharyngodon idellus). The grass carp lectin possesses a molecular mass of 205 kDa. It is composed of six subunits each with a molecular mass of 35 kDa. The N-terminal amino acid sequence of the grass carp shows similarity to those of other fish species with 26-35% amino acid identity. It is mitogenic toward murine splenocytes and peritoneal exudate cells.

Reversible metabolism of drugs

Many drugs undergo reversible metabolism. The basis of our understanding of this process is the reversible metabolism of prednisone (PD)-prednisolone (PL). The pharmacokinetics of reversible metabolism requires the use of four area under the curve values integrated into four equations for clearance (CL). Other variables, such as linear versus non-linear disposition, can play important roles in reversible metabolism. Of recent interest is the reversible metabolism of haloperidol which consists of an interconversion process between the parent drug haloperidol (HL) and its reduced metabolite (RH). However, the interconversion of HL-RH differs from the PD-PL model in that, whereas PD and PL are both active, RH is considered to be a therapeutically inactive, possibly toxic, metabolite. This article reviews the pharmacodynamic and pharmacokinetic properties of HL and RH and the possible clinical effects that can result from this reversible metabolism.

Solenin, a novel protein with translation-inhibiting activity from the traditional Chinese medicinal fish, the sea dragon Solenognathus hardwickii

A single-chained protein designated solenin was isolated from Solenognathus hardwickii, a fish used as traditional Chinese medicinal material. Solenin was capable of inhibiting translation in a cell-free rabbit reticulocyte lysate system with an IC(50) of 2 microM and expressing a ribonuclease activity of 0.8U/mg toward yeast transfer RNA, but it lacked N-glycosidase activity characteristic of ribosome inactivating proteins Solenin exhibited a molecular weight of 18kDa and possessed an N-terminal sequence AHDAEVNEVKAQVAA. The protein was adsorbed on three types of chromatographic media: Affi-gel blue gel, CM-Sepharose and Mono S. It was devoid of antifungal and lectin activities.

Lack of CYP3A4 inhibition by grapefruit juice and ketoconazole upon clozapine administration in vivo

The drug-food and drug-drug interaction between grapefruit juice (GFJ) and ketoconazole (KETO) was evaluated in schizophrenic patients given a single dose of clozapine (CLZ). CLZ is metabolized primarily by CYP isozymes 3A4 and 1A2 to two principal metabolites, desmethylclozapine (DCLZ) and clozapine N-oxide (CNO). GFJ and KETO are well known potent CYP 3A4 inhibitors in the gastrointestinal tract and hepatic isozymes, respectively. Twenty-one schizophrenic patients participated in the co-administration of CLZ 50 mg and GFJ. After a one-week washout, five patients were given double the GFJ (HGFJ) dose for 7 consecutive days. In another group of five patients, ketoconazole (KETO) 400 mg was given for 7 consecutive days. At the end of the 7-day period for both groups, CLZ was coadministered with the HGFJ and KETO groups. CLZ, DCLZ and CNO were assayed by HPLC. GFJ, HGJF and ketoconazole failed to significantly change CLZ disposition. Metabolites DCLZ and CNO concentrations remained unchanged during the study. The only exception was decreased Cmax in DCLZ and CNO concentrations. These results indicate that CYP 3A4 inhibition may not be clinically significant compared to CYP 1A2, as previous studies show a dramatic increase in CLZ plasma concentrations with fluvoxamine (CYP 1A2 inhibitor). The reasons for the lack of drug-food and drug-drug interactions with CLZ and CYP 3A4 inhibitors can be explained by the higher Ki values for gastrointestinal and hepatic CYP 3A4 isozymes.

Isolation of a novel agglutinin with complex carbohydrate binding specificity from fresh fruiting bodies of the edible mushroom Lyophyllum shimeiji

A hemagglutinin, with a molecular weight of 30,000 and expressing hemagglutinating activity which could not be inhibited by simple sugars and glycoproteins, was isolated from fresh fruiting bodies of the edible mushroom Lyophyllum shimeiji. The protein was adsorbed on CM-Sepharose even in 20 mM ammonium acetate (pH 5.5) containing 1 M NaCl and was desorbed by 20 mM ammonium bicarbonate (pH 9). The hemagglutinating activity was subsequently adsorbed on Mono S in 20 mM ammonium acetate (pH 5.5) and was desorbed by a linear gradient of 0.2-0.5 M NaCl in ammonium acetate buffer. The hemagglutinin exhibited a novel N-terminal sequence not found in any lectin and hemagglutinin reported so far. It was devoid of antifungal activity.

Antiproliferative and antimitogenic activities in a peptide from puffball mushroom Calvatia caelata

A peptide with a molecular weight of 8 kDa and an N-terminal sequence closely resembling that of ubiquitin was isolated from fruiting bodies of the mosaic puffball mushroom Calvatia caelata. The peptide was purified using a protocol that involved ion-exchange chromatography on DEAE-cellulose, affinity chromatography on Affi-gel blue gel, and ion-exchange chromatography on Mono S. The peptide inhibited translation in the cell-free rabbit reticulocyte lysate system and exhibited N-glycosidase activity. It potently inhibited proliferation of spleen cells with an IC(50) of about 100 nM as indicated by the suppression of [methyl-(3)H]thymidine uptake. The viability of breast cancer cells was reduced to half at a ubiquitin concentration of about 100 nM.

A monomeric mannose-binding lectin from inner shoots of the edible chive (Allium tuberosum)

A mannose-binding lectin was isolated from the inner shoots of the chive Allium tuberosum. The procedure involved aqueous extraction, (NH4)2SO4 precipitation, dialysis to remove (NH4)2SO4, affinity chromatography on mannose-agarose, ion exchange chromatography on SP-Sepharose, gel filtration on Superdex 75, and ion exchange chromatography on Mono S. Lectin activity was adsorbed on mannose-agarose, SP-Sepharose, and Mono S. The lectin demonstrated a molecular weight of 13 kDa in sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration, indicating that it is a single-chain protein. N-terminal sequence analysis revealed its remarkable homology to Allium cepa lectin and similarity to a lesser extent to lectins from members of the Amaryllidaceae, Orchidaceae, and Liliaceae. The lectin manifested mitogenic activity in murine splenocytes and inhibitory activity against human immunodeficiency virus type 1 reverse transcriptase.

Branded versus generic clozapine: bioavailability comparison and interchangeability issues

Clozapine has been the treatment of choice for patients with refractory schizophrenia. Generic clozapine has recently become available, because of a waiver of the usual criteria for establishing bioequivalence. However, there are biopharmaceutical, bioavailability, and clinical concerns related to the generic formulation raised by both clinicians and academic researchers. We conducted a prospective, randomized, crossover study to evaluate steady-state pharmacokinetics, pharmacodynamics, and tolerability of generic clozapine (Zenith Goldline Pharmaceuticals) versus Clozaril (Novartis Pharmaceuticals) in schizophrenic patients. A preliminary report of the pertinent bioavailability results is presented here. Despite comparable mean plasma concentration-time curves, significant differences were found in the primary pharmacokinetic parameters of the 2 formulations in almost 40% of patients. Such intraindividual differences raise the issue of average bioequivalence versus individual bioequivalence and the implication for interchangeability of different clozapine formulations. The decision to switch a patient from branded to generic clozapine should be made on an individual basis with special emphasis on clinical outcome, and patients should be monitored closely during the transition.

A robust cysteine-deficient chitinase-like antifungal protein from inner shoots of the edible chive Allium tuberosum

From the inner shoots of the chive Allium tuberosum, a single-chained protein with a molecular weight of 36 kDa and an N-terminal sequence manifesting resemblance to chitinases but lacking in cysteine residues characteristic of a cysteine-rich domain present in chitinases of other Allium species, was purified. The isolation procedure entailed affinity chromatography on Affi-gel blue gel, ion-exchange chromatography on DEAE-cellulose and Mono S, and gel filtration on Superdex 75. The protein was unadsorbed on DEAE-cellulose and adsorbed on Affi-gel blue gel and Mono S. It exhibited antifungal activity against Rhizoctonia solani, Fusarium oxysporum, Coprinus comatus, Mycosphaerella arachidicola, and Botrytis cinerea. The IC(50) for its antifungal effect against Botrytis cinerea was 0.2 microM. The antifungal activity was stable after 1 h at pH 1.6 and 12.3, and up to 60 degrees C for 5 min. Incubation of the protein with trypsin or chymotrypsin at an enzyme:substrate ratio of 1:100 and pH 7.6 up to 150 min did not affect its antifungal activity. The protein did not exhibit antibacterial activity. The protein inhibited cell-free translation in a rabbit reticulocyte system with an IC(50) of 0.8 microM, but did not affect the proliferation of mouse splenocytes. It exerted some cytotoxic effect on breast cancer cells and was inhibitory toward HIV-1 reverse transcriptase.

Surface diffusion coefficients for room acoustics: free-field measures

A surface diffusion coefficient is needed in room acoustics to enable the quality of diffusing surfaces to be evaluated. It may also facilitate more accurate geometric room acoustic models. This paper concentrates on diffusion coefficients derived from free-field polar responses. An extensive set of two- and three-dimensional measurements and predictions was used to test the worth of different diffusion coefficient definitions. The merits and problems associated with these types of coefficients are discussed, and past parameters reviewed. Two new coefficients are described. The new measure based on the autocorrelation function is forwarded as the best free-field coefficient. The strengths and weaknesses of the coefficient are defined.

From a profiled diffuser to an optimized absorber

The quadratic residue diffuser was originally designed for enhanced scattering. Subsequently, however, it has been found that these diffusers can also be designed to produce exceptional absorption. This paper looks into the absorption mechanism of the one-dimensional quadratic residue diffuser. A theory for enhanced absorption is presented. Corresponding experiments have also been done to verify the theory. The usefulness of a resistive layer at the well openings has been verified. A numerical optimization was performed to obtain a better depth sequence. The results clearly show that by arranging the depths of the wells properly in one period, the absorption is considerably better than that of a quadratic residue diffuser.

The adaptive beam-tracing algorithm

The most popular models to predict sound propagation in architectural spaces involve the tracing of rays, images, or beams. Most current beam-tracing methods use conical or triangular beams that may produce overlaps and holes in the predicted sound field. Hence a new method has been developed whereby the shape of reflected beams is governed by the shape of reflecting surfaces so as to produce a geometrically perfect description of the sound propagation for halls with occluding surfaces. The method also facilitates the calculation of diffuse sound propagation by managing the energy transfer from a specular model to a diffuse model. This adaptive beam-tracing method compares well with other methods in terms of speed and accuracy.

Imaging membrane potential with voltage-sensitive dyes

Membrane potential can be measured optically using a variety of molecular probes. These measurements can be useful in studying function at the level of an individual cell, for determining how groups of neurons generate a behavior, and for studying the correlated behavior of populations of neurons. Examples of the three kinds of measurements are presented. The signals obtained from these measurements are generally small. Methodological considerations necessary to optimize the resulting signal-to-noise ratio are discussed.

Photoinduced dehydrogenation of defects in undoped a-si:H using positron annihilation spectroscopy

We report changes in variable-energy positron annihilation spectroscopy measurements on undoped hydrogenated amorphous silicon films after light soaking. The change, seen predominantly in the high momentum band of the annihilation radiation, is not reversed by thermal annealing. We suggest, following recent models of the Staebler-Wronski effect, that light exposure induces hydrogen trapped in vacancylike defects to become mobile in the Si network. The observations place constraints on models of hydrogen motion fitting macroscopic Staebler-Wronski effect kinetics and may help to achieve a definitive description of metastability in a-Si:H.

Odors elicit three different oscillations in the turtle olfactory bulb

We measured the spatiotemporal aspects of the odor-induced population response in the turtle olfactory bulb using a voltage-sensitive dye, RH414, and a 464-element photodiode array. In contrast with previous studies of population activity using local field potential recordings, we distinguished four signals in the response. The one called DC covered almost the entire area of the olfactory bulb; in addition, three oscillations, named rostral, middle, and caudal according to their locations, occurred over broad regions of the bulb. In a typical odor-induced response, the DC signal appeared almost immediately after the start of the stimulus, followed by the middle oscillation, the rostral oscillation, and last, the caudal oscillation. The initial frequencies of the three oscillations were 14.1, 13.0, and 6.6 Hz, respectively. When the rostral and caudal oscillations occurred together, their frequencies differed by a factor of 1.99 +/- 0.01. The following evidence suggests that the four signals are functionally independent: (1) in different animals some signals could be easily detected whereas others were undetectable; (2) the four signals had different latencies and frequencies; (3) the signals occurred in different locations and propagated in different directions; (4) the signals responded differently to changes in odor concentration; (5) the signals had different shapes; and (6) the rostral and caudal signals added in a simple, linear manner in regions where the location of the two signals overlapped. However, the finding that the frequency of the rostral oscillation is precisely two times that of the caudal oscillation suggests a significant relationship between the two. The location of the caudal oscillation in the bulb changed from cycle to cycle, implying that different groups of neurons are active in different cycles. This result is consistent with the earlier findings in the olfactory system of the locust (). Our results suggest an additional complexity of parallel processing of olfactory input by multiple functional population domains.

Clinical pharmacology of dopamine agonists

With the availability of newer dopamine agonists selective for dopamine (D2) receptor subtypes, medical management of Parkinson's disease has progressed substantially. These agents can decrease the frequency of ergot-related side effects and dyskinesias. Also, when given as adjunctive therapy with levodopa, they can allow the levodopa maintenance dosage to be reduced without loss of symptom control. Based on early clinical experience, dopamine agonists can also be prescribed as initial monotherapy and can delay therapy with levodopa. Their therapeutic roles will be defined further by long-term studies.

CYP2D6 inhibition by fluoxetine, paroxetine, sertraline, and venlafaxine in a crossover study: intraindividual variability and plasma concentration correlations

The authors report the CYP2D6 inhibitory effects of fluoxetine, paroxetine, sertraline, and venlafaxine in an open-label, multiple-dose, crossover design. Twelve CYP2D6 extensive metabolizers were phenotyped, using the dextromethorphan/dextrorphan (DM/DX) urinary ratio, before and after administration of fluoxetine 60 mg (loading dose strategy), paroxetine 20 mg, sertraline 100 mg, and venlafaxine 150 mg. Paroxetine, sertraline, and venlafaxine sequences were randomized with 2-week washouts between treatments; fluoxetine was the last antidepressant (AD) administered. Comparing within groups, baseline DM/DX ratios (0.017) were significantly lower than DM/DX ratios after treatment (DM/DXAD) with fluoxetine (0.313, p < 0.0001) and paroxetine (0.601, p < 0.0001) but not for sertraline (0.026, p = 0.066) or venlafaxine (0.023, p = 0.485). Between groups, DM/DXAD ratios were significantly higher for fluoxetine and paroxetine compared to sertraline and venlafaxine. No differences between DM/DXAD ratios were found for fluoxetine and paroxetine although more subjects phenocopied to PM status after receiving the latter (42% vs. 83%; chi 2 = 4.44, p = 0.049, df = 1). Similarly, no differences between DM/DXAD ratios were found for sertraline and venlafaxine. Of note, the DM/DXAD for 1 subject was much lower after treatment with paroxetine (0.058) compared to fluoxetine (0.490), while another subject exhibited a much lower ratio after treatment with fluoxetine (0.095) compared to paroxetine (0.397). Significant correlations between AD plasma concentration and DM/DXAD were found for paroxetine (r2 = 0.404, p = 0.026) and sertraline (r2 = 0.64, p = 0.002) but not fluoxetine or venlafaxine. In addition, DM/DXAD correlated with baseline isoenzyme activity for paroxetine, sertraline, and venlafaxine groups. These results demonstrate the potent, but variable, CYP2D6 inhibition of fluoxetine and paroxetine compared to sertraline and venlafaxine. CYP2D6 inhibition may be related, in part, to dose, plasma concentration, and baseline isoenzyme activity, and these correlations merit further investigation.