bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive analysis of co-occurring domain sets in yeast proteins
Authors: Cohen-Gihon Inbar , Nussinov Ruth , Sharan Roded
Published: June 2007

Background

Protein domains are fundamental evolutionary units of protein architecture, composing proteins in a modular manner. Combinations of two or more, possibly non-adjacent, domains are thought to play specific functional roles within proteins. Indeed, while the number of potential co-occurring domain sets (CDSs) is very large, only a few of these occur in nature. Here we study the principles governing domain content of proteins, using yeast as a model species.

Results

We design a novel representation of proteins and their constituent domains as a protein-domain network. An analysis of this network reveals 99 CDSs that occur in proteins more than expected by chance. The identified CDSs are shown to preferentially include ancient domains that are conserved from bacteria or archaea. Moreover, the protein sets spanned by these combinations were found to be highly functionally coherent, significantly match known protein complexes, and enriched with protein-protein interactions. These observations serve to validate the biological significance of the identified CDSs.

Conclusion

Our work provides a comprehensive list of co-occurring domain sets in yeast, and sheds light on their function and evolution.
The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms
Authors: Kiraga Joanna , Mackiewicz Pawel , Mackiewicz Dorota , Kowalczuk Maria , Biecek Przemysław , Polak Natalia , Smolarczyk Kamila , Dudek Miroslaw R , Cebrat Stanislaw
Published: June 2007

Background

The distribution of isoelectric point (pI) of proteins in a proteome is universal for all organisms. It is bimodal dividing the proteome into two sets of acidic and basic proteins. Different species however have different abundance of acidic and basic proteins that may be correlated with taxonomy, subcellular localization, ecological niche of organisms and proteome size.

Results

We have analysed 1784 proteomes encoded by chromosomes of Archaea, Bacteria, Eukaryota, and also mitochondria, plastids, prokaryotic plasmids, phages and viruses. We have found significant correlation in more than 95% of proteomes between the protein length and pI in proteomes – positive for acidic proteins and negative for the basic ones. Plastids, viruses and plasmids encode more basic proteomes while chromosomes of Archaea, Bacteria, Eukaryota, mitochondria and phages more acidic ones. Mitochondrial proteomes of Viridiplantae, Protista and Fungi are more basic than Metazoa. It results from the presence of basic proteins in the former proteomes and their absence from the latter ones and is related with reduction of metazoan genomes. Significant correlation was found between the pI bias of proteomes encoded by prokaryotic chromosomes and proteomes encoded by plasmids but there is no correlation between eukaryotic nuclear-coded proteomes and proteomes encoded by organelles. Detailed analyses of prokaryotic proteomes showed significant relationships between pI distribution and habitat, relation to the host cell and salinity of the environment, but no significant correlation with oxygen and temperature requirements. The salinity is positively correlated with acidicity of proteomes. Host-associated organisms and especially intracellular species have more basic proteomes than free-living ones. The higher rate of mutations accumulation in the intracellular parasites and endosymbionts is responsible for the basicity of their tiny proteomes that explains the observed positive correlation between the decrease of genome size and the increase of basicity of proteomes. The results indicate that even conserved proteins subjected to strong selectional constraints follow the global trend in the pI distribution.

Conclusion

The distribution of pI of proteins in proteomes shows clear relationships with length of proteins, subcellular localization, taxonomy and ecology of organisms. The distribution is also strongly affected by mutational pressure especially in intracellular organisms.
Lack of association between the chemokine receptor 5 polymorphism CCR5delta32 in rheumatoid arthritis and juvenile idiopathic arthritis
Authors: Lindner Ewald , Nordang Gry BN , Melum Espen , Flatø Berit , Selvaag Anne Marit , Thorsby Erik , Kvien Tore K , Førre Øystein T , Lie Benedicte A
Published: June 2007

Background

The chemokine receptor CCR5 has been detected at elevated levels on synovial T cells, and a 32 bp deletion in the CCR5 gene leads to a non-functional receptor. A negative association between the CCR5Δ32 and rheumatoid arthritis (RA) has been reported, although with conflicting results. In juvenile idiopathic arthritis (JIA), an association with CCR5 was recently reported. The purpose of this study was to investigate if the CCR5Δ32 polymorphism is associated with RA or JIA in Norwegian cohorts.

Methods

853 RA patients, 524 JIA patients and 658 controls were genotyped for the CCR5Δ32 polymorphism.

Results

The CCR5Δ32 allele frequency was 11.5% in the controls vs. 10.4% in RA patients (OR = 0.90; P = 0.36) and 9.7% in JIA patients (OR = 0.85; P = 0.20). No decreased homozygosity was observed for CCR5Δ32, as previously suggested.

Conclusion

Our data do not support an association between the CCR5Δ32 allele and Norwegian RA or JIA patients. Combining our results with those from a recently published meta-analysis still provide evidence for a role for CCR5Δ32 in RA, albeit substantially weaker than the effect first reported.
Production of in vitro amplified DNA pseudolibraries and high-throughput cDNA target amplification
Authors: Frey Daniel , Kambach Christian , Steinmetz Michel O , Jaussi Rolf
Published: June 2007

Background

Many structural biology- and high-throughput laboratories experience the acquisition of multiple cDNAs from different sources as a rather time- and resource-consuming procedure. The techniques presented here solve these problems.

Results

An advanced target cDNA amplification procedure employing RNA- or cDNA-derived pseudolibraries circumvents the usual DNA transfection during library establishment. A small sample of reverse transcribed ss- or ds-cDNA or DNA from a pre-existing library is multiplied by in vitro rolling circle ramification amplification. The resulting cDNA pseudolibrary serves as a template for numerous highly efficient PCR amplifications and permits production and analysis of target cDNAs on an automated liquid handling workstation.

Conclusion

The overall efficiency of the simple protocol collection approaches 100% for targets from libraries with low complexity such as Drosophila and yields >80% of amplicons up to 3 kb size in the case of human cDNA.
Chaperone-based procedure to increase yields of soluble recombinant proteins produced in E. coli
Authors: de Marco Ario , Deuerling Elke , Mogk Axel , Tomoyasu Toshifumi , Bukau Bernd
Published: June 2007

Background

The overproduction of recombinant proteins in host cells often leads to their misfolding and aggregation. Previous attempts to increase the solubility of recombinant proteins by co-overproduction of individual chaperones were only partially successful. We now assessed the effects of combined overproduction of the functionally cooperating chaperone network of the E. coli cytosol on the solubility of recombinant proteins.

Results

A two-step procedure was found to show the strongest enhancement of solubility. In a first step, the four chaperone systems GroEL/GroES, DnaK/DnaJ/GrpE, ClpB and the small HSPs IbpA/IbpB, were coordinately co-overproduced with recombinant proteins to optimize de novo folding. In a second step, protein biosynthesis was inhibited to permit chaperone mediated refolding of misfolded and aggregated proteins in vivo. This novel strategy increased the solubility of 70% of 64 different heterologous proteins tested up to 42-fold.

Conclusion

The engineered E. coli strains and the two-step procedure presented here led to a remarkable increase in the solubility of a various recombinant proteins and should be applicable to a wide range of target proteins produced in biotechnology.
Validation and cultural adaptation of a German version of the Physicians' Reactions to Uncertainty scales
Authors: Schneider Antonius , Szecsenyi Joachim , Barie Stefan , Joest Katharina , Rosemann Thomas
Published: June 2007

Background

The aim of the study was to examine the validity of a translated and culturally adapted version of the Physicians' Reaction to Uncertainty scales (PRU) in primary care physicians.

Methods

In a structured process, the original questionnaire was translated, culturally adapted and assessed after administering it to 93 GPs. Test-retest reliability was tested by sending the questionnaire to the GPs again after two weeks.

Results

The principal factor analysis confirmed the postulated four-factor structure underlying the 15 items. In contrast to the original version, item 5 achieved a higher loading on the 'concern about bad outcomes' scale. Consequently, we rearranged the scales. Good item-scale correlations were obtained, with Pearson's correlation coefficient ranging from 0.56–0.84. As regards the item-discriminant validity between the scales 'anxiety due to uncertainty' and 'concern about bad outcomes', partially high correlations (Pearson's correlation coefficient 0.02–0.69; p < 0.001) were found, indicating an overlap between both constructs. The assessment of internal consistency revealed satisfactory values; Cronbach's alpha of the rearranged version was 0.86 or higher for all scales. Test-retest-reliability, assessed by means of the intraclass-correlation-coefficient (ICC), exceeded 0.84, except for the 'reluctance to disclose mistakes to physicians' scale (ICC = 0.66). In this scale, some substantial floor effects occurred, with 29.3% of answers showing the lowest possible value.

Conclusion

Dealing with uncertainty is an important issue in daily practice. The psychometric properties of the rearranged German version of the PRU are satisfying. The revealed floor effects do not limit the significance of the questionnaire. Thus, the German version of the PRU could contribute to the further evaluation of the impact of uncertainty in primary care physicians.
In vivo optical imaging of integrin αV-β3 in mice using multivalent or monovalent cRGD targeting vectors
Authors: Jin Zhao-Hui , Josserand Véronique , Foillard Stéphanie , Boturyn Didier , Dumy Pascal , Favrot Marie-Christine , Coll Jean-Luc
Published: June 2007

Background

The cRGD peptide is a promising probe for early non-invasive detection of tumors. This study aimed to demonstrate how RAFT-c(-RGDfK-)4, a molecule allowing a tetrameric presentation of cRGD, improved cRGD-targeting potential using in vivo models of αVβ3-positive or negative tumors.

Results

We chose the human embryonic kidney cells HEK293(β3) (high levels of αVβ3) or HEK293(β1) (αVβ3-negative but expressing αV and β1) engrafted subcutaneously (s.c.) in mice. Non-invasive in vivo optical imaging demonstrated that as compared to its monomeric cRGD analogue, Cy5-RAFT-c(-RGDfK-)4 injected intravenously had higher uptake, prolonged retention and markedly enhanced contrast in HEK293(β3) than in the HEK293(β1) tumors. Blocking studies further demonstrated the targeting specificity and competitive binding ability of the tetramer.

Conclusion

In conclusion, we demonstrated that Cy5-RAFT-c(-RGDfK-)4 was indeed binding to the αVβ3 receptor and with an improved activity as compared to its monomeric analog, confirming the interest of using multivalent ligands. Intravenous injection of Cy5-RAFT-c(-RGDfK-)4 in this novel pair of HEK293(β3) and HEK293(β1) tumors, provided tumor/skin ratio above 15. Such an important contrast plus the opportunity to use the HEK293(β1) negative control cell line are major assets for the community of researchers working on the design and amelioration of RGD-targeted vectors or on RGD-antagonists.
Clearance of low levels of HCV viremia in the absence of a strong adaptive immune response
Authors: Meyer Manuela F , Lehmann Marc , Cornberg Markus , Wiegand Johannes , Manns Michael P , Klade Christoph , Wedemeyer Heiner
Published: June 2007

Spontaneous clearance of hepatitis C virus (HCV) has frequently been associated with the presence of HCV-specific cellular immunity. However, there had been also reports in chimpanzees demonstrating clearance of HCV-viremia in the absence of significant levels of detectable HCV-specific cellular immune responses. We here report seven asymptomatic acute hepatitis C cases with peak HCV-RNA levels between 300 and 100.000 copies/ml who all cleared HCV-RNA spontaneously. Patients were identified by a systematic screening of 1176 consecutive new incoming offenders in a German young offender institution. Four of the seven patients never developed anti-HCV antibodies and had normal ALT levels throughout follow-up. Transient weak HCV-specific CD4+ T cell responses were detectable in five individuals which did not differ in strength and breadth from age- and sex-matched patients with chronic hepatitis C and long-term recovered patients. In contrast, HCV-specific MHC-class-I-tetramer-positive cells were found in 3 of 4 HLA-A2-positive patients. Thus, these cases highlight that clearance of low levels of HCV viremia is possible in the absence of a strong adaptive immune response which might explain the low seroconversion rate after occupational exposure to HCV.
Porcine adenovirus type 3 E1Blarge protein downregulates the induction of IL-8
Authors: Zhou Yan , Ficzycz Andrew , Tikoo Suresh Kumar
Published: June 2007

Replication-defective (E1-E3 deleted) adenovirus vector based gene delivery results in the induction of cytokines including IL-8, which may contribute to the development of inflammatory immune responses. Like other adenoviruses, E1 + E3 deleted porcine adenovirus (PAdV) 3 induces the production of IL-8 in infected cells. In contrast, no IL-8 production could be detected in cells infected with wild-type or mutant PAdV-3s containing deletion in E1A + E3 (PAV211) or E1Bsmall+ E3 (PAV212). Expression of PAdV-3 E1Blargeinhibited the NF-κB dependent transcription of luciferase from IL-8 promoter. Imunofluorescence and electrophoretic mobility shift assays suggested that constitutive expression of PAdV-3 E1Blargeinhibited the nuclear translocation of NF-κB and its subsequent binding to DNA. These results suggest that E1Blargeinteracts with NF-κB to prevent transcription and down regulate proinflammatory cytokine IL-8 production.
HLA class II DR and DQ genotypes and haplotypes associated with rheumatic fever among a clinically homogeneous patient population of Latvian children
Authors: Stanevicha Valda , Eglite Jelena , Zavadska Dace , Sochnevs Arturs , Shantere Ruta , Gardovska Dace
Published: June 2007

The HLA system is being paid more and more attention because it is very significant in polymorphous immunological reactions. Several studies have suggested that genetic susceptibility to rheumatic fever (RF) and rheumatic heart disease (RHD) is linked to HLA class II alleles. We hypothesized that HLA class II associations within RHD may be more consistent if analysed amongst patients with a relatively homogeneous clinical outcome. A total of 70 RF patients under the age of 18 years were surveyed and analysed in Latvia. HLA genotyping of DQA1, DQB1 and DRB1 was performed using PCR with amplification with sequence-specific primers. We also used results from a previous study of DQB1 and DRB1 genotyping. In the RF patients, HLA class II DQA1*0401 was found more frequently compared to DQA1*0102. In the RF homogeneous patient groups, DQA1*0402 has the highest odds ratio. This is also the case in the multivalvular lesion (MVL) group, together with DQA1*0501 and DQA1*0301. In the chorea minor patients, DQA1*0201 was often found. Significant HLA DQA1 protective genotypes were not detected, although DQA1 genotypes *0103/*0201 and *0301/*0501 were found significantly and frequently. In the distribution of HLA DRB1/DQA1 genotypes, *07/*0201 and *01/*0501 were frequently detected; these also occurred significantly often in the MVL group. The genotype *07/*0201 was frequently found in Sydenhamn's chorea patients that had also acquired RHD, but DRB1*04/DQA1*0401 was often apparent in RF patients without RHD. In the distribution of HLA DQA1/DQB1 genotypes, both in RF patients and in the homogeneous patient groups, the least frequent were *0102/*0602-8. The genotype DQA1*0501 with the DQB1 risk allele *0301 was often found in the MVL group. The genotype *0301/*0401-2 was frequently found in the RF and Sydenhamn's chorea patient groups. The haplotype *07-*0201-*0302 was frequently found in RF and homogeneous patient groups, including the MVL group. In addition, haplotypes *04-*0401-*0301 and *04-*0301-*0401-2 were frequent amongst patients with Sydenhamn's chorea. The protective alleles DQA1*0102 and DQB1*0602-8 in the haplotype DRB1*15 were less frequently found in RF patients. The results of the present study support our hypothesis and indicate that certain HLA class II haplotypes are associated with risk for or protection against RHD and that these associations are more evident in patients in clinically homogeneous groups.
Injurious mechanical ventilation in the normal lung causes a progressive pathologic change in dynamic alveolar mechanics
Authors: Pavone Lucio A , Albert Scott , Carney David , Gatto Louis A , Halter Jeffrey M , Nieman Gary F
Published: June 2007

Introduction

Acute respiratory distress syndrome causes a heterogeneous lung injury, and without protective mechanical ventilation a secondary ventilator-induced lung injury can occur. To ventilate noncompliant lung regions, high inflation pressures are required to 'pop open' the injured alveoli. The temporal impact, however, of these elevated pressures on normal alveolar mechanics (that is, the dynamic change in alveolar size and shape during ventilation) is unknown. In the present study we found that ventilating the normal lung with high peak pressure (45 cmH20) and low positive end-expiratory pressure (PEEP of 3 cmH2O) did not initially result in altered alveolar mechanics, but alveolar instability developed over time.

Methods

Anesthetized rats underwent tracheostomy, were placed on pressure control ventilation, and underwent sternotomy. Rats were then assigned to one of three ventilation strategies: control group (n = 3, Pcontrol = 14 cmH2O, PEEP = 3 cmH2O), high pressure/low PEEP group (n = 6, Pcontrol = 45 cmH2O, PEEP = 3 cmH2O), and high pressure/high PEEP group (n = 5, Pcontrol = 45 cmH2O, PEEP = 10 cmH2O). In vivo microscopic footage of subpleural alveolar stability (that is, recruitment/derecruitment) was taken at baseline and than every 15 minutes for 90 minutes following ventilator adjustments. Alveolar recruitment/derecruitment was determined by measuring the area of individual alveoli at peak inspiration (I) and end expiration (E) by computer image analysis. Alveolar recruitment/derecruitment was quantified by the percentage change in alveolar area during tidal ventilation (%I – EΔ).

Results

Alveoli were stable in the control group for the entire experiment (low %I – EΔ). Alveoli in the high pressure/low PEEP group were initially stable (low %I – EΔ), but with time alveolar recruitment/derecruitment developed. The development of alveolar instability in the high pressure/low PEEP group was associated with histologic lung injury.

Conclusion

A large change in lung volume with each breath will, in time, lead to unstable alveoli and pulmonary damage. Reducing the change in lung volume by increasing the PEEP, even with high inflation pressure, prevents alveolar instability and reduces injury. We speculate that ventilation with large changes in lung volume over time results in surfactant deactivation, which leads to alveolar instability.
Functional coordination of alternative splicing in the mammalian central nervous system
Authors: Fagnani Matthew , Barash Yoseph , Ip Joanna Y , Misquitta Christine , Pan Qun , Saltzman Arneet L , Shai Ofer , Lee Leo , Rozenhek Aviad , Mohammad Naveed , Willaime-Morawek Sandrine , Babak Tomas , Zhang Wen , Hughes Timothy R , van der Kooy Derek , Frey Brendan J , Blencowe Benjamin J
Published: June 2007

Background

Alternative splicing (AS) functions to expand proteomic complexity and plays numerous important roles in gene regulation. However, the extent to which AS coordinates functions in a cell and tissue type specific manner is not known. Moreover, the sequence code that underlies cell and tissue type specific regulation of AS is poorly understood.

Results

Using quantitative AS microarray profiling, we have identified a large number of widely expressed mouse genes that contain single or coordinated pairs of alternative exons that are spliced in a tissue regulated fashion. The majority of these AS events display differential regulation in central nervous system (CNS) tissues. Approximately half of the corresponding genes have neural specific functions and operate in common processes and interconnected pathways. Differential regulation of AS in the CNS tissues correlates strongly with a set of mostly new motifs that are predominantly located in the intron and constitutive exon sequences neighboring CNS-regulated alternative exons. Different subsets of these motifs are correlated with either increased inclusion or increased exclusion of alternative exons in CNS tissues, relative to the other profiled tissues.

Conclusion

Our findings provide new evidence that specific cellular processes in the mammalian CNS are coordinated at the level of AS, and that a complex splicing code underlies CNS specific AS regulation. This code appears to comprise many new motifs, some of which are located in the constitutive exons neighboring regulated alternative exons. These data provide a basis for understanding the molecular mechanisms by which the tissue specific functions of widely expressed genes are coordinated at the level of AS.
Improved Overall Survival in Postmenopausal Women With Early Breast Cancer After Anastrozole Initiated After Treatment With Tamoxifen Compared With Continued Tamoxifen: The ARNO 95 Study
Authors: Kaufmann Manfred , Jonat Walter , Hilfrich Jörn , Eidtmann Holger , Gademann Günther , Zuna Ivan , von Minckwitz Gunter
Published: June 2007

Purpose

In postmenopausal women with estrogen receptor–positive early breast cancer, surgery is usually followed by a 5-year course of tamoxifen. This report presents results of a prospective, open-label, randomized study, designed to evaluate the benefits of switching to anastrozole after 2 years of tamoxifen treatment, compared with continuing on tamoxifen for 5 years.

Patients and Methods

After receiving tamoxifen treatment for 2 years, eligible patients (n = 979) were randomly assigned to switch to anastrozole (1 mg/d) or continue tamoxifen (20 or 30 mg/d) for an additional 3 years. Patients were monitored every 6 months during years 1 to 3 and annually thereafter. The primary efficacy variable was disease-free survival, including local or distant recurrence, new contralateral breast cancer, or death. Secondary variables were overall survival and assessment of safety.

Results

Switching to anastrozole resulted in a significant reduction in the risk of disease recurrence (hazard ratio [HR], 0.66; 95% CI, 0.44 to 1.00; P = .049), and improved overall survival (HR, 0.53; 95% CI, 0.28 to 0.99; P = .045) compared with continuing on tamoxifen. Fewer patients who switched to anastrozole reported serious adverse events (22.7% v 30.8%) compared with those who continued on tamoxifen, mainly due to more patients in the tamoxifen group with endometrial events. The overall safety profile for anastrozole was consistent with previous reports and no new safety issues were identified.

Conclusion

Postmenopausal women who have taken tamoxifen for 2 years as adjuvant therapy are less likely to experience a recurrence of breast cancer and have improved overall survival if they switch to anastrozole compared with continuing to receive tamoxifen.
Stratification of Breast Cancer Risk in Women With Atypia: A Mayo Cohort Study
Authors: Degnim Amy C. , Visscher Daniel W. , Berman Hal K. , Frost Marlene H. , Sellers Thomas A. , Vierkant Robert A. , Maloney Shaun D. , Pankratz V. Shane , de Groen Piet C. , Lingle Wilma L. , Ghosh Karthik , Penheiter Lois , Tlsty Thea , Melton L. Joseph , Reynolds Carol A. , Hartmann Lynn C.
Published: June 2007

Purpose

Atypical hyperplasia is a well-recognized risk factor for breast cancer, conveying an approximately four-fold increased risk. Data regarding long-term absolute risk and factors for risk stratification are needed.

Patients and Methods

Women with atypical hyperplasia in the Mayo Benign Breast Disease Cohort were identified through pathology review. Subsequent breast cancers were identified via medical records and a questionnaire. Relative risks (RRs) were estimated using standardized incidence ratios, comparing the observed number of breast cancers with those expected based on Iowa Surveillance, Epidemiology, and End Results (SEER) data. Age, histologic factors, and family history were evaluated as risk modifiers. Plots of cumulative breast cancer incidence provided estimates of risk over time.

Results

With mean follow-up of 13.7 years, 66 breast cancers (19.9%) occurred among 331 women with atypia. RR of breast cancer with atypia was 3.88 (95% CI, 3.00 to 4.94). Marked elevations in risk were seen with multifocal atypia (eg, three or more foci with calcifications [RR, 10.35; 95% CI, 6.13 to 16.4]). RR was higher for younger women (< 45; RR, 6.76; 95% CI, 3.24 to 12.4). Risk was similar for atypical ductal and atypical lobular hyperplasia, and family history added no significant risk. Breast cancer risk remained elevated over 20 years, and the cumulative incidence approached 35% at 30 years.

Conclusion

Among women with atypical hyperplasia, multiple foci of atypia and the presence of histologic calcifications may indicate “very high risk” status (> 50% risk at 20 years). A positive family history does not further increase risk in women with atypia.
Role of p53 in antioxidant defense of HPV-positive cervical carcinoma cells following H2O2 exposure
Authors: Ding Boxiao , Chi Sung Gil , Kim Se Heon , Kang Suki , Cho Jae Ho , Kim Dong Su , Cho Nam Hoon
Published: June 2007

In HPV-positive cervical carcinoma cells, p53 protein is functionally antagonized by the E6 oncoprotein. We investigated a possible role of p53 in antioxidant defense of HPV-positive cervical cancer cell lines. We found that SiHa cells containing integrated HPV 16 had higher expression of p53 and exhibited the greatest resistant to H2O2-induced oxidative damage, compared with HeLa, CaSki and ME180 cell lines. Downregulation of p53 resulted in the inhibition of p53-regulated antioxidant enzymes and elevated intracellular ROS in SiHa cells. By contrast, the ROS level was not affected in HeLa, CaSki and ME180 cell lines after inhibition of the p53 protein. Under mild or severe H2O2-induced stress, p53-deficient SiHa cells exhibited much higher ROS levels than control SiHa cells. Furthermore, we analyzed cell viability and apoptosis after H2O2 treatment and found that p53 deficiency sensitized SiHa cells to H2O2 damage. Inhibition of p53 resulted in excessive oxidation of DNA; control SiHa cells exhibited a more rapid removal of 8-oxo-7,8-dihydro-2′-deoxyguanosine from DNA compared with p53-deficient SiHa cells exposed to the same level of H2O2 challenge. These data collectively show that endogenous p53 in SiHa cells has an antioxidant function and involves in the reinforcement of the antioxidant defense.
Distinct Guest-Dependent Changes in Arrangements of a Fluorophore and the Corresponding Emission Modes in a Ternary System: Transcription and Translation of Guest Molecular Information
Authors: Mizobe Yuji , Hinoue Tomoaki , Miyata Mikiji , Hisaki Ichiro , Hasegawa Yasuchika , Tohnai Norimitsu
Published: June 2007

In order to prepare novel molecular arrangements of a fluorophore that result in new solid-state fluorescence properties, we fabricated a ternary system consisting of anthracene-2,6-disulfonic acid (ADS), aliphatic primary amines and guest molecules as a fluorophore, arrangement-controlling parts and molecular information sources, respectively. The system consisting of ADS, (rac)-s-butylamine and 1,4-dioxane yielded a novel zigzag arrangement of anthracene moieties that gave rise to a rare emission mode. Subsequent screening of the amines and guests in the ternary system suggested that a relationship exists among the molecular information source, the zigzag arrangement and the rare emission mode. Namely, molecular information of 1,4-dioxane is transcribed to the zigzag arrangement, and the arrangement is translated into the excimer-like emission. Interestingly, the relationship appears to mimic that found in DNA. In addition, transcription of the molecular information requires the appropriate shape and size of void spaces formed by ADS and (rac)-s-butylamine. From these observations, the zigzag arrangement and the corresponding rare emission mode is specific for the system of ADS, (rac)-s-butylamine and 1,4-dioxane.
Surface Modification of Titania Particles with Urushiol (Japanese Lacquer) and Its Application to the Preparation of Polymer–Titania Hybrids
Authors: Suzuki Takeyuki , Ito Yusuke , Boury Bruno , Sugahara Yoshiyuki
Published: June 2007

To prepare stable polymer–titania hybrids, titania particles were modified using urushiol (extracted from Japanese lacquer) via surface complexation. The urushiol moieties underwent hydrosilylation and radical graft-polymerization to yield polymer–titania hybrids in which the titania particles were dispersed in polymer matrices.
Selective Precipitation of Salts on the Surface of a Gel State Phosphatidylcholine Membrane
Authors: Iijima Kazutoshi , Matsubara Teruhiko , Sato Toshinori
Published: June 2007

We identified precipitates of salts on phospholipid bilayers in solution with an atomic force microscope and X-ray fluorescence analyzer. The precipitates on the surface of a dipalmitoyl phosphatidylcholine membrane in a gel state were found in Tris-buffered saline and grew with time. The salts precipitated were considered to be NaCl in buffer.
Preparation and Reaction of Phenylsulfonyl-substituted Dizinciomethane
Authors: Baba Yoko , Toshimitsu Akio , Matsubara Seijiro
Published: June 2007

Treatment of dibromomethyl phenyl sulfone with zinc powder in the presence of a catalytic amount of lead in THF afforded phenylsulfonyl-substituted dizinciomethane. The species converts a ketone or aldehyde into an alkenyl sulfone via a Wittig-type olefination reaction with the assistance of β-TiCl3.
Structural and Magnetic Properties of Co–Ni Nanowire Array Prepared by Alternating Current Electrodeposition
Authors: Xu Jinxia , Wang Keyu , Xu Yi
Published: June 2007

Ordered Co43Ni57 nanowire array has been fabricated in a porous alumina template by alternating current electrodeposition. The as-obtained nanowires exhibit a diameter of about 45 nm and aspect ratio of more than 30. X-ray diffraction indicates that the Co43Ni57 nanowires crystallize in Co (fcc) solid solution with a highly preferential orientation (111). The Co43Ni57 nanowire array has an obvious magnetic anisotropy. However, the magnetic properties of such nanowire arrays exhibited a bad thermal stability at the medium temperature of 200 °C.
Immobilization of Palladium Acetate on Ionic Liquid Copolymerized Polystyrene: A Way to Eliminate Inhibiting Effect of Imidazolium Chloride and Enhance Catalytic Performance
Authors: Sugimura Rie , Qiao Kun , Tomida Daisuke , Kume Yohei , Yokoyama Chiaki
Published: June 2007

Immobilization of palladium acetate on a novel polymeric support that is prepared by copolymerization of 3-butyl-1-vinylimidazolium chloride with styrene is demonstrated to be an effective way to eliminate inhibiting effect of imidazolium chloride and enhance catalytic performance.
Characteristics of Amorphous TiO2 Particles Prepared in Various Reaction Systems
Authors: Takayanagi Mariko , Imai Yoko , Tajima Kazuo
Published: June 2007

Amorphous TiO2 particles were prepared by the various reverse systems such as reverse micelle, reverse microemulsion, reverse emulsion, and by the sol–gel method, and investigated on their photocatalytic properties. After calcinating for 3 h at 200 °C, we found that they indicated two kinds of band-gap energies and gave the photocatalytic activity with irradiation of either UV or visible light, while anatase state did not work with visible light. However, any amorphous states were gradually converted into crystalline anatase with continuous irradiation, even without heating.
Pd–Au Bimetal Supported on Rutile–TiO2 for Selective Synthesis of Hydrogen Peroxide by Oxidation of H2 with O2 under Atmospheric Pressure
Authors: Ishihara Tatsumi , Hata Yuiko , Nomura Yohei , Kaneko Kenji , Matsumoto Hiroshige
Published: June 2007

Rutile TiO2 support is effective for increasing the formation rate as well as selectivity to H2O2. A great enhancement in the H2O2 formation rate and selectivity is achieved by controlling the particle size of Pd–Au (7:3 in weight ratio) alloy, and the average size of 18 nm exhibits the high selectivity to H2O2 under atmospheric pressure.
Magic-angle-spinning NMR at 30 T with a Hybrid Magnet
Authors: Hashi Kenjiro , Shimizu Tadashi , Fujito Teruaki , Goto Atsushi , Ohki Shinobu , Shimoda Keiji , Tobu Yasuhiro , Saito Koji
Published: June 2007

Solid-state NMR measurements at 30 T have been performed with a hybrid magnet of National Institute for Materials Science. Spectral resolution less than 3 ppm was confirmed by 79Br magic-angle-spinning (MAS) NMR measurements of a reference material KBr. A small sample and an aluminum metal shield were used to reduce the effects of field inhomogeneity and fluctuation. As an example of application for an industrial material, 27Al MAS NMR of a refractory mortar was demonstrated.
New Method for Synthesis of Aldehydes from Esters by Sodium Diisobutyl-t-butoxyaluminum Hydride
Authors: Song Jung In , An Duk Keun
Published: June 2007

A new reducing agent, sodium diisobutyl-t-butoxyaluminum hydride (SDBBA), easily prepared by addition of sodium t-butoxide to DIBALH in THF at 0 °C or room temperature, readily reacts with representative esters to give the corresponding aldehydes in very good yields under mild conditions (0 °C).
Theory and Experiment in Mass Spectrometry: A Perspective on the Relationship between Computational Modelling and Experiment in Gas-Phase Ion Chemistry
Authors: Uggerud Einar
Published: June 2007

In this lecture/paper we will discuss the somewhat complicated relationship between theory and experiment in molecular science in general and mass spectrometry in particular, illustrated by some recent literature examples.
Quadrupole Ion Traps and Trap Arrays: Geometry, Material, Scale, Performance
Authors: Ouyang Z. , Gao L. , Fico M. , Chappell W.J. , Noll R.J. , Cooks R.G.
Published: June 2007

Quadrupole ion traps are reviewed, emphasizing recent developments, especially the investigation of new geometries, guided by multiple particle simulations such as the ITSIM program. These geometries include linear ion traps (LITs) and the simplified rectilinear ion trap (RIT). Various methods of fabrication are described, including the use of rapid prototyping apparatus (RPA), in which 3D objects are generated through point-by-point laser polymerization. Fabrication in silicon using multilayer semiconductor fabrication techniques has been used to construct arrays of micro-traps. The performance of instruments containing individual traps as well as arrays of traps of various sizes and geometries is reviewed. Two types of array are differentiated. In the first type, trap arrays constitute fully multiplexed mass spectrometers in which multiple samples are examined using multiple sources, analyzers and detectors, to achieve high throughput analysis. In the second, an array of individual traps acts collectively as a composite trap to increase trapping capacity and performance for a single sample. Much progress has been made in building miniaturized mass spectrometers; a specific example is a 10kg hand-held tandem mass spectrometer based on the RIT mass analyzer. The performance of this instrument in air and water analysis, using membrane sampling, is described.
Microdevices in Mass Spectrometry
Authors: Foret F. , Kusý P.
Published: June 2007

Miniaturization of laboratory instrumentation is becoming critical in achieving the speed and throughput required by the current revolutionary progress in biology. This mini review critically summarizes the present status of microfluidic devices designed for use in mass spectrometry.
Mass Spectrometry in the Detection and Diagnosis of Congenital Disorders of Glycosylation
Authors: Wada Yoshinao
Published: June 2007

Mass spectrometry (MS) of large molecules such as proteins and oligosaccharides has not been employed in clinical practices, while that of small metabolites is widely used for the screening and diagnosis of various congenital diseases. Congenital disorders of glycosylation (CDG) is a newly recognized group of diseases derived from defects in the biosynthetic pathway of protein glycosylation and the patients are never decisively diagnosed unless the glycoprotein molecules are analyzed. We have constructed a diagnostic system where MS of glycoproteins and glycopeptides identifies abnormalities in their glycan moieties. This program is anticipated to reveal the prevalence of CDG and to demonstrate the essential role of MS in the emerging field of medicine, disease glycomics and glycoproteomics.
Analysis of Melt Copolymers
Authors: Montaudo Maurizio S.
Published: June 2007

Melt copolymer chains are the main (most abundant) reaction product obtained when heating a blend of two (or more) condensation polymers (such as polyester + polycarbonate or polyester + polyamide or polyester + polyester) in which exchange reactions occur. In fact, during the melt-mixing reaction, an AB copolymer is formed and, as a consequence, the sample is a complex mixture made of three components or simply “parts”, referred to as Z1, Z2 and Z3, where Z1 and Z2 are the parts for unreacted homopolymers (A and B), whereas Z3 is the part for the copolymer. In this paper, it is shown that matrix-assisted laser desorption/ionization mass spectrometry (and mass spectrometry in general) can be used to monitor the yield of the reactive blending reaction, YR, by measuring the amount of unreacted homopolymer (Z1 and Z2). In order to allow for comparisons, the paper also discusses conventional methods for measuring Z1 and Z2, such as liquid chromatography and nuclear magnetic resonance.
Accurate Mass as a Bioinformatic Parameter in Data-to-Knowledge Conversion: Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Peptide De Novo Sequencing
Authors: Spengler B.
Published: June 2007

With the availability of ultra-precise mass spectrometric biomolecular data, the accurate mass is becoming a physical quantity of high interest for bioinformatics tools and strategies. Fourier transform ion cyclotron resonance mass spectrometry with electrospray ionization or matrix-assisted laser desorption/ionization sources now allows the easy determination of amino acid composition of medium size, unknown peptides when employing combinatorial calculation of hypothetical parent and fragment ion masses. This new method, which in a second step, allows the reliable de-novo sequencing of completely unknown peptides [“composition-based sequencing (CBS)”1] appears to open a wide new field of bioanalytical investigation. It has been shown that even unspecifically cleaved proteins can be identified easily and reliably when accurate mass evaluation is combined with protein database search tools.2 It is quite clear that, while the nominal mass of a peptide has obviously no useful correlation to biomolecular structure, the accurate mass, instead, has a strong and direct correlation to structure that so far has not been exploited considerably by bioinformatic tools. It has already become obvious that accurate mass evaluation is going to become a central goal for bioinformatics strategies in the near future.3–11 Strategies for extracting structural, and even functional, information out of accurate mass values of biomolecules still have to be developed. Examples and prospects of accurate mass evaluation in bioinformatics for the field of proteomics are outlined in the following.
Selected Ion Flow Tube Mass Spectrometry for On-Line Trace Gas Analysis in Biology and Medicine
Authors: Španěl P. , Smith D.
Published: June 2007

Selected ion flow tube mass spectrometry, (SIFT-MS), is a technique for simultaneous real-time quantification of several trace gases in air and exhaled breath. It relies on chemical ionization of the trace gas molecules in air/breath samples introduced into helium carrier gas, using H3O+, NO+ and O2+ reagent (precursor ions). Reactions between the precursor ions and the trace gas molecules proceed for an accurately defined time, the precursor and product ions being detected and counted by a downstream mass spectrometer. Absolute concentrations of trace gases in single breath exhalation can be determined by SIFT-MS down to parts-per-billion (ppb) levels, obviating sample collection into bags or onto traps. Calibration using chemical standards is not required, as the concentrations are calculated using the known reaction rate constants and measured flow rates and pressures. SIFT-MS has been used for many pilot investigations in several areas of research, especially as a non-invasive breath analysis tool to investigate physiological processes in humans and animals, for clinical diagnosis and for therapeutic monitoring. Examples of the results obtained from several such studies are outlined to demonstrate the potential of SIFT-MS for trace gas analysis of air, exhaled breath and the headspace above liquids.
Proteomic Strategies for Rapid Characterization of Micro-Organisms
Authors: Fenselau C. , Russell S. , Swatkoski S. , Edwards N.
Published: June 2007

Bioinformatic considerations are offered to illustrate strengths and limitations of the characterization of Bacillus spores based on proteomic interpretation of matrix-assisted laser desorption/ionization spectra. In particular, species-specific biomarkers are evaluated in the context of both experimental access and uniqueness in silico.
Modeling Deoxyribonucleic Acid and Ribonucleic Acid Damage in the Gas Phase
Authors: Tureček František
Published: June 2007

This short review outlines the tandem mass spectrometric methods for the generation and analysis of transient nucleobase radicals relevant to deoxyribonucleic acid and ribonucleic acid damage. Radical hydrogen atom adducts to uracil, adenine, cytosine and N-methylcytosine were generated by femtosecond electron transfer to the corresponding gas-phase cations in fast beams at 8 keV kinetic energy. Radical unimolecular dissociations were monitored by product analysis following collisional ionization to cations or anions using neutralization-reionization mass spectrometry. The radical energetics and dissociation kinetics were further analyzed by mapping the potential energy surfaces by high-level ab initio calculations in combination with Rice-Remsberger-Kassel-Marcus calculations of unimolecular rate constants. This first-principles-based approach allows one to model radical dissociations occurring from doublet ground electronic states of radical intermediates, assign reaction mechanisms and derive quantitative branching ratios for dissociation channels that are in agreement with experiments. Theoretical analysis also provides distinction between radical dissociations occurring on the ground and excited electronic state potential energy surfaces. Specific characterization of excited state dissociations of nucleobase and other polyatomic radicals remains a challenging topic for both experimentalists and computational chemists.
Metabolomics and Metabolite Profiling: Past Heroes and Future Developments
Authors: Griffiths W.J. , Karu K. , Hornshaw M. , Woffendin G. , Wang Y.
Published: June 2007

Following the sequencing of the human and other genomes, much research effort is now invested in post-genomic science, particularly in the related disciplines of proteomics and metabolomics. In this paper, we will attempt to provide an overview of mass spectrometry-based metabolomic strategies, discuss the evolution of metabolomics from its predecessor, “metabolite profiling”, and provide some pointers to future methodological and technological direction. Current data from the authors' laboratory will also be presented, highlighting our efforts in the field of “targeted metabolomics”, namely, “steroidomics in the brain”.
Discrimination of Storage Duration of Apples Stored in a Cooled Room and Shelf-Life by Visible-Near Infrared Spectroscopy
Authors: Camps C. , Guillermin P. , Mauget J.C. , Bertrand D.
Published: June 2007

Improved non-destructive instrumental approaches for grading fruit during post-harvest could be an efficient way to monitor stock in the apple industry. The objective of this study was to evaluate the ability of visible-near infrared (vis-NIR) spectroscopy in reflectance mode for classifying apples left on the shelf or stored in a cooled room. The ability of NIR spectroscopy to classify the duration of storage of three apple cultivars in two storage modalities was evaluated. A total of 450 fruit, sampled after 7, 14, 28, 60, 90 and 120 days of storage in a cooled room (CR) and 7, 14 and 28 days in shelflife (SL), has been studied. The classification of these modalities was analysed by factorial discriminant analysis (FDA) pooling the spectral data of all cultivars (global models) into a common data set. Then, the cultivar effect on the classification of the same modalities was analysed by processing data from each cultivar in separate factorial descriminant analyses. A preliminary analysis showed the genetic variability of spectral data due to the three apple cultivars. We show that vis-NIR spectroscopy allowed the correct classification of the fruits of each cultivar by more than 95%. The classification relied on both vis and NIR absorption bands: 500, 680, 1400 to 1700, 1850, 1950, 2200 and 2300 nm. We show that storage modalities of global models can be classified by more than 75% and 83% for fruits stored in a cooled room and shelf, respectively. Classification of the same storage modalities was improved by cultivar models with percentage of individuals correctly classified of 86% (Gala), 89% (Elstar) and 85% (Smoothee) for fruits stored in a cooled room and 95% (Gala), 98% (Elstar) and 95% (Smoothee) for fruits left in shelflife. We conclude that despite the slight increase of efficiency of the models when we considered each apple cultivar separately, global models applicable to a set of different cultivars presents a correct level of classification and could be usefull for some commercial applications.
Near Infrared Spectroscopic Analysis of Foundry Moulding and Core Sands
Authors: Dungan Robert S. , Reeves James B.
Published: June 2007

Sands coated, mixed and polymerised with a wide variety of materials are used to make moulds and cores for the casting of metals. Heating results in the production of a wide variety of organic materials by pyrolysis. These resulting compounds may need to be characterised before waste sands can be beneficially used in the environment. The objective of this work was to examine the potential of near infrared (NIR) spectroscopy to qualitatively identify organic residues in waste green sands (clay-bonded moulding sand). Examination of spectra of waste green sands, burnt and unburnt cores and components used in producing sands for the foundry industry have demonstrated that NIR spectroscopy has potential for use to confirm the identity and composition of source materials. Additional research is needed to determine if NIR spectroscopy can be successfully used to quantify organics present in waste foundry sands.