Identification of nasopharyngeal carcinoma antigens that induce humoral immune response by proteomic analysis

A proteomics-based approach has been used to identify proteins that commonly elicit a humoral immune response in nasopharyngeal carcinoma (NPC). Sera from 19 newly diagnosed NPC patients and 19 healthy individuals were analyzed for IgG autoantibodies against NPC proteins resolved by 2-DE. Protein spots that exhibited selective reactivity with sera from NPC patients were identified by MS. Among nine identified proteins, cytokeratin 19 (CK19), Erb3 binding protein (EBP1), and Rho GDP dissociation inhibitor-beta (Rho-GDI-2) induced autoantibodies in more than 36.8% of NPC patients but not in healthy individuals. Furthermore, Western blot analysis and immunohistochemical staining were performed to determine the expression and localization of CK19, EBP1, and Rho-GDI-2 in NPC and normal nasopharyngeal mucosal tissues. Up-regulated CK19 and EBP1, but not Rho-GDI-2, were observed in NPC vs. normal tissue. Subcellular localization of the three proteins in NPC tissue was same as that in the normal tissue. Thus, overexpression of CK19 and EBP1 may be one of the mechanisms for their autoantibody development in NPC. To validate the findings of a proteomic analysis, occurrence of autoantibodies against these three proteins was detected by immunoprecipitation and Western blot analysis in additional 30 NPC patients, 23 other types of cancer patients and 20 healthy individuals. Results showed that frequency of autoantibodies against CK19, EBP1 and Rho-GDI-2 in NPC patients was significantly higher than that in other types of cancer patients and healthy individuals. We conclude that CK19, EBP1 and Rho-GDI-2 may have utility in NPC screening and diagnosis.     

Quantification of heart fatty acid binding protein as a biomarker for drug-induced cardiac and musculoskeletal necroses

Heart fatty acid binding protein (Fabp3) is a cytosolic protein expressed primarily in heart, and to a lesser extent in skeletal muscle, brain, and kidney. During myocardial injury, the Fabp3 level in serum is elevated rapidly, making it an ideal early marker for myocardial infarction. In this study, an MS‐based selected reaction monitoring method (LC‐SRM) was developed for quantifying Fabp3 in rat serum. Fabp3 was enriched first through an immobilized antibody, and the protein was digested on beads directly. A marker peptide of Fabp3 was quantified using LC‐SRM with a stable isotope‐labeled peptide standard. For six quality control samples with Fabp3 ranging from 0.256 to 25 ng, the average recovery following the procedure was about 73%, and the precision (%CV) between replicates was less than 7%. The Fabp3 concentrations in rat serum peaked 1 h after isoproterenol treatment, and returned to baseline levels 24 h after the dose. Elevated Fabp3 levels were also detected in rats administered with a PPAR α/δ agonist, which has shown to cause skeletal muscle necrosis. Fabp3 can be used as a biomarker for both cardiac and skeletal necroses. The cross‐validation of the LC‐SRM method with an existing ELISA method is described.     

A proteome analysis of the dorsolateral prefrontal cortex in human alcoholic patients

Alcoholic patients commonly experience cognitive decline. It is postulated that cognitive dysfunction is caused by an alcohol-induced region-selective brain damage, particularly to the prefrontal region, and grey and white matter may be affected differently. We used a proteomics-based approach to compare protein expression profiles of the dorsolateral prefrontal cortex (Brodmann area 9 (BA9)) from human alcoholic and healthy control brains. Changes in the relative expression of 110 protein 'spots' were identified in the BA9 grey matter, of which 54 were identified as 44 different proteins. In our recent article, 60 protein spots were differentially expressed in the BA9 white matter and 18 of these were identified (Alexander-Kaufman, K., James, G., Sheedy, D., Harper, C., Matsumoto, I., Mol. Psychiatry 2006, 11, 56-65). Additional BA9 white matter proteins are identified here and discussed in conjunction to our grey matter results. Thiamine-dependent enzymes transketolase and pyruvate dehydrogenase (E1β ubunit) were among the proteins identified. To our knowledge, this is the first time a disruption in thiamine-dependent enzymes has been demonstrated in the brains of 'neurologically uncomplicated' alcoholics. By identifying protein expression changes in prefrontal grey and white matter separately, hypotheses may draw upon more mechanistic explanations as to how alcoholism causes the structural alterations associated with alcohol-related brain damage and cognitive dysfunction.     

The discovery of biomarkers for type 2 diabetic nephropathy by serum proteome analysis

Diabetic nephropathy (DN) is a serious kidney complication of diabetes, and constitutes the leading cause of end-stage renal disease. The earliest clinical evidence of DN is microalbuminuria, a term which refers to the appearance of small but abnormal amounts of albumin in the urine. However, screening methods for DN, such as biomarker assays, are yet to be developed for type 2 DN. In the present study, in an attempt to identify the biomarkers for initial diagnoses of type 2 DN, the protein profiles of human sera collected from 30 microalbuminuric type 2 diabetic patients were compared with those collected from 30 normoalbuminuric type 2 diabetic patients, via 2-DE. As a result, a total of 18 spots were determined to have different protein levels in the microalbuminuric patients. Twelve spots had lower protein levels of approximately 50%, and the other six had higher levels of approximately 100-300% as compared to the spots of normoalbuminuric patients. These spots were identified with ESI-Q-TOF (ESI-quadrupole-TOF) MS. Among the identified proteins, vitamin D-binding protein (DBP) and pigment epithelium-derived factor (PEDF) were verified by Western blotting. The results of this study indicate that the DBP may be employed as diagnostic and monitoring biomarkers of type 2 DN, contingent on further study into the matter.     

Large-scale protein identification of human urine proteome by multi-dimensional LC and MS/MS

Urine is a human specimen that is easily obtained non-invasively for clinical diagnosis. We attempted to enhance the resolution of current human urine proteomes and construct a comprehensive reference database for advanced studies, such as the discovery of biomarkers for renal diseases. Multi-dimensional LC-MS/MS was coupled with de novo sequencing and database matching. The proposed approach improved the identification of not only the proteins, but also the post-translational sites of urinary proteins. We identified 165, 200 and 259 unique gene products in the urine proteomes from males, females and pregnant women, respectively. When all of the results were combined and the redundancies removed, a total of 1095 distinct peptides were identified. Of these, 1016 peptides were associated with 334 unique gene products. In this study, over 100 gene products, including some disease-related proteins, were detected in urine for the first time by proteomic approaches. Various proteins with novel post-translational hydroxylation were identified using the MASCOT program and de novo sequencing. All proteins with peptide information were summarized into a comprehensive urine protein database. We believe that this comprehensive urine proteome database will assist in the identification of urinary proteins/polypeptides whose spectra are difficult to interpret in the discovery of urinary biomarkers.     

A base62 transformation format of ISO 10646 for multilingual identifiers

ISO 10646 Universal Character Set (UCS) is a 31‐bit coding architecture that covers symbols in most of the world's written languages. Identifiers in programming languages are usually defined by using alphanumeric characters of ASCII, which represent mainly English words. An approach for working around this deficiency is to encode multilingual identifiers into the alphanumeric range of ASCII. For case‐sensitive languages, an encoding that utilizes [0–9][A–Z][a–z] can be more space‐efficient for multilingual identifiers. This paper proposes a base62 transformation format of ISO 10646 called UTF‐62. The resulting string of UTF‐62 is within a [0–9][A–Z][a–z] range, a total of 62 base characters. UTF‐62 also preserves the lexicographic sorting order of UCS‐4. Copyright © 2001 John Wiley & Sons, Ltd.     

Response to ‘Comments on: A cohesion measure for object‐oriented classes’

Indicating that CBMC does not satisfy the monotonic property in terms of the number of interactions, Xu and Zhou proposed an augmented definition of CBMC by adopting cut set instead of glue methods. The augmented CBMC clearly satisfies the monotonic property. However, CBMC is designed to overcome the problem with respect to the number of interactions and, therefore, focuses on the interaction pattern, especially, member connectivity. Consequently, it does not make sense to mention the monotonic property of CBMC with respect to interaction number. Moreover, the notion of glue methods allows several interpretations on the design quality of a class. However, that meaningful interpretation is not possible for the augmented definition due to the removal of the notion of glue methods. Copyright © 2001 John Wiley & Sons, Ltd.     

New oxide phosphors for FEDs: Ruddlesden—Popper phases synthesized with IIIB‐group elements

Abstract— A red‐emitting phosphor, SrTiO³:Pr³⁺, for low‐voltage‐type FEDs and VFDs was developed by Futaba Corporation in 1996. The addition of Al or Ga is essential in the preparation of this phosphor because it improves the luminescence efficiency dramatically. For this impurity effect, Futaba Corporation proposed a charge‐compensation mechanism, which was supported by a recent observation of emission lines due to Al³⁺‐Pr³⁺ pairs. In addition, it was found that Al also works as a scavenger of planar defects, presumably SrO thin layers interleaved in the SrTiO³ lattice, by forming strontium aluminates. The latter mechanism suggests the possibility that a similar impurity effect can be found in materials with crystal structures, including alkaline‐earth oxide layers (Ruddlesden‐Popper phases).     

Improvement of luminance and luminous efficacy in PDPs

Abstract— The dependence of PDP luminance and efficacy on the input power was investigated for several Xe‐Ne gas mixtures. The input power was varied in two ways: namely, by changing the dielectric‐layer capacitance (thickness) and by changing the sustain voltage. A distinctly different behavior was found; for increasing capacitance the efficacy decreases markedly, whereas for increasing sustain voltage the efficacy increases. A design window comprising the combination of a high Xe concentration and a high sustain voltage was suggested. In this window, a high luminance and a high efficacy are concurrent. A 4‐in. test panel with 10% Xe in Ne has been realized showing a white luminance of 2040 cd/m² and an efficacy of 2.3 lm/W for continuous sustaining at 50 kHz with a sustain voltage of 225 V.     

STABILIZATION OF A CLASS OF NONLINEAR NON‐MINIMUM PHASE SYSTEMS

This paper tackles the problem of stabilization of a class of non‐minimum phase nonlinear systems which have zero dynamics with an eigenvalue zero of multiplicity 2. By adding some new terms, called cross terms, we are able to generalize the concept of the Lyapunov function with a homogeneous derivative along the trajectory, which was introduced in [4], to produce a suitable Lyapunov function. The Lyapunov function assures that the stability of an approximate system, which consists of some lower order terms of a nonlinear system with an eigenvalue zero of multiplicity 2, implies the stability of the whole system. Applying these to non‐minimum phase zero dynamics of nonlinear systems with such a center, a sufficient condition and a design method of state feedback control are obtained for stabilizing the systems.