bluuebunny/crossref_metadata_2025 huggingface dataset:
Physiological Characterization of a Heme-Deficient Mutant of
Staphylococcus aureus
by a Proteomic Approach
Authors: Kohler Christian , von Eiff Christof , Peters Georg , Proctor Richard A. , Hecker Michael , Engelmann Susanne
Published: November 2003

The high-resolution two-dimensional (2D) protein gel electrophoresis technique combined with matrix-assisted laser desorption ionization-time of flight mass spectrometry was used for identification of proteins whose levels were changed by a mutation in
hemB
. Cytoplasmic protein extracts obtained from the mutant and the wild type (strain COL) at different stages of growth in tryptone soya broth (exponential, transitional, and stationary growth phases) were separated on 2D protein gels. Comparison of the 2D patterns of the protein extracts of the two strains revealed major differences. Because the electron transport chain of the mutant is interrupted due to the deficiency of heme, this organism should be unable to use oxygen or nitrate as a terminal electron acceptor. Consistent with this hypothesis, proteins involved in the glycolytic pathway and related pathways (glyceraldehyde-3-phosphate dehydrogenase, enolase, and phosphoglycerate kinase) and in fermentation pathways (lactate dehydrogenase, alcohol dehydrogenase, and pyruvate formate lyase) were induced in exponentially growing cells of the mutant. These results strongly indicate that the
hemB
mutant generates ATP from glucose or fructose only by substrate phosphorylation. Analyses of the fermentation reactions showed that the main product was lactate. Although pyruvate formate lyase (Pfl) and pyruvate dehydrogenase were present, neither ethanol nor acetate was detected in significant amounts. Presumably, Pfl was not activated in the presence of oxygen, and pyruvate dehydrogenase might have very low activity. Transcriptional analysis of
citB
, encoding the aconitase, revealed that the activity of the citrate cycle enzymes was down-regulated in the
hemB
mutant. The arginine deiminase pathway was also induced, and it could provide ATP as well. Furthermore, the amounts of most of the extracellular virulence factors were significantly reduced by a mutation in
hemB
, which is consistent with previous reports.
Identification and Characterization of Genes Required for Biosynthesis and Transport of the Siderophore Vibrioferrin in
Vibrio parahaemolyticus
Authors: Tanabe Tomotaka , Funahashi Tatsuya , Nakao Hiroshi , Miyoshi Shin-Ichi , Shinoda Sumio , Yamamoto Shigeo
Published: November 2003

In response to low iron availability,
Vibrio parahaemolyticus
synthesizes and secretes a polyhydroxycarboxylate-type siderophore vibrioferrin which is composed of 1 mol each of 2-ketoglutaric acid,
l
-alanine, ethanolamine, and citric acid. We have previously reported the cloning and characterization of the
pvuA
gene, which encodes the 78-kDa outer membrane receptor protein for ferric vibrioferrin. In this study, nine genes involved in the biosynthesis and transport of vibrioferrin have been identified in the genomic regions surrounding the
pvuA
gene. The genes were sequenced, and gene disruptants were constructed by insertion mutation for phenotype analysis. Five of the genes, named
pvsABCDE
, constitute an operon that is expressed under iron-limiting conditions. Homology searches of their predicted protein products suggested that the four genes
pvsABDE
are implicated in the biosynthesis of the siderophore. Another gene in the same operon,
pvsC
, encodes a putative exporter that is homologous to members of the major facilitator superfamily of multidrug efflux pumps. The remaining four genes, named
pvuBCDE
, encode proteins strongly homologous to
Escherichia coli
FecBCDE, respectively, which are components of the ATP-binding cassette transporter system for ferric dicitrate. Reverse transcriptase PCR analysis revealed that these transport genes are transcribed as a single mRNA with the upstream genes,
psuA
and
pvuA
. Phenotypic comparison between the wild-type strain and its targeted gene disruptants supported the biological functions for the respective operons that were expected on the basis of the homology search.
Role of theSalmonellaPathogenicity Island 1 (SPI-1) Protein InvB in Type III Secretion of SopE and SopE2, TwoSalmonellaEffector Proteins Encoded Outside of SPI-1
Authors: Ehrbar Kristin , Friebel Andrea , Miller Samuel I. , Hardt Wolf-Dietrich
Published: November 2003

Salmonella entericasubspecies 1 serovar Typhimurium encodes a type III secretion system (TTSS) withinSalmonellapathogenicity island 1 (SPI-1). This TTSS injects effector proteins into host cells to trigger invasion and inflammatory responses. Effector proteins are recognized by the TTSS via signals encoded in their N termini. Specific chaperones can be involved in this process. The chaperones InvB, SicA, and SicP are encoded in SPI-1 and are required for transport of SPI-1-encoded effectors. Several key effector proteins, like SopE and SopE2, are located outside of SPI-1 but are secreted in an SPI-1-dependent manner. It has not been clear how these effector proteins are recognized by the SPI-1 TTSS. Using pull-down and coimmunoprecipitation assays, we found that SopE is copurified with InvB, the known chaperone for the SPI-1-encoded effector protein Sip/SspA. We also found that InvB is required for secretion and translocation of SopE and SopE2 and for stabilization of SopE2 in the bacterial cytosol. Our data demonstrate that effector proteins encoded within and outside of SPI-1 use the same chaperone for secretion via the SPI-1 TTSS.
Pinpointing Biphenyl Dioxygenase Residues That Are Crucial for Substrate Interaction
Authors: Zielinski Marco , Kahl Silke , Hecht Hans-Jürgen , Hofer Bernd
Published: November 2003

Three regions of the biphenyl dioxygenase (BDO) of
Burkholderia
sp. strain LB400 have previously been shown to significantly influence the interaction between enzyme and substrates at the active site. For a further discrimination within these regions, we investigated the effects of 23 individual amino acid exchanges. The regiospecificity of substrate dioxygenation was used as a sensitive means to monitor changes in the steric-electronic structure of the active site. Replacements of residues that, according to a model of the BDO three-dimensional structure, directly interact with substrates in most, but not all, cases (Met231, Phe378, and Phe384) very strongly altered this parameter (by factors of >7). On the other hand, a number of amino acids (Ile243, Ile326, Phe332, Pro334, and Trp392) which have no contacts with substrates also strongly changed the site preference of dioxygenation (by factors of between 2.6 and 3.5). This demonstrates that residues which had not been predicted to be influential can play a pivotal role in BDO specificity.
Crystal Structure of
Bacillus subtilis
α-Amylase in Complex with Acarbose
Authors: Kagawa Masayuki , Fujimoto Zui , Momma Mitsuru , Takase Kenji , Mizuno Hiroshi
Published: November 2003

The crystal structure of
Bacillus subtilis
α-amylase, in complex with the pseudotetrasaccharide inhibitor acarbose, revealed an hexasaccharide in the active site as a result of transglycosylation. After comparison with the known structure of the catalytic-site mutant complexed with the native substrate maltopentaose, it is suggested that the present structure represents a mimic intermediate in the initial stage of the catalytic process.
The Phosphotransferase System of
Streptomyces coelicolor
Is Biased for
N
-Acetylglucosamine Metabolism
Authors: Nothaft Harald , Dresel Dagmar , Willimek Andreas , Mahr Kerstin , Niederweis Michael , Titgemeyer Fritz
Published: November 2003

Mutation of the
crr-ptsI
gene locus revealed that
Streptomyces coelicolor
uses the phosphotransferase system (PTS) for
N
-acetylglucosamine uptake.
crr
,
ptsI
, and
ptsH
, which encode the three general PTS phosphotransferases, are induced by
N
-acetylglucosamine but not by other PTS substrates. Thus, the
S. coelicolor
PTS is biased for
N
-acetylglucosamine utilization, a novel feature that distinguishes this PTS from others.
Highly Conjugative pMG1-Like Plasmids Carrying Tn
1546
-Like Transposons That Encode Vancomycin Resistance in
Enterococcus faecium
Authors: Tomita Haruyoshi , Tanimoto Koichi , Hayakawa Satoshi , Morinaga Kyoko , Ezaki Kohji , Oshima Hisaji , Ike Yasuyoshi
Published: November 2003

A total of 12 VanA-type vancomycin-resistant enterococci, consisting of 10
Enterococcus faecium
isolates and two
Enterococcus avium
isolates, were examined in detail. The vancomycin resistance conjugative plasmids pHTα (65.9 kbp), pHTβ (63.7 kbp), and pHTγ (66.5 kbp) were isolated from each of three different
E. faecium
strains. The plasmids transferred highly efficiently between enterococcus strains during broth mating and were homologous with pMG1 (Gm
r
; 65.1 kb).
Extending production models to include process error in the population dynamics
Authors: Punt Andre E
Published: November 2003

Four methods for fitting production models, including three that account for the effects of error in the population dynamics equation (process error) and when indexing the population (observation error), are evaluated by means of Monte Carlo simulation. An estimator that represents the distributions of biomass explicitly and integrates over the unknown process errors numerically (the NISS estimator) performs best of the four estimators considered, never being the worst estimator and often being the best in terms of the medians of the absolute values of the relative errors. The total-error approach outperforms the observation-error estimator conventionally used to fit dynamic production models, and the performance of a Kalman filter based estimator is particularly poor. Although the NISS estimator is the best-performing estimator considered, its estimates of quantities of management interest are severely biased and highly imprecise for some of the scenarios considered.
Horizontal and vertical distribution patterns, retention rates, and population dynamics of zooplankton on Western Bank, Scotian Shelf
Authors: Reiss Christian S , McLaren Ian A , Avendaño Patricia
Published: November 2003

We assess the importance of retention rates and local production to the concentration of zooplankton on Western Bank, Scotian Shelf, during September and October 1998. We do so using (i) particle retention rates derived from an array of 25 current meters and inferences from hydrographic structure; (ii) observations on the horizontal and vertical distribution of zooplankton and ichthyoplankton; and (iii) a simple projection-matrix model of the population dynamics of two copepod species, Centropages typicus and Pseudocalanus spp. Zooplankton biomass and adult stages of copepods were more abundant in surface waters on the bank (p < 0.05) at broad (25 km) spatial scales. Zooplankton was correlated with ichthyoplankton abundance at this scale (r > 0.5, p < 0.001), a result of local production of both zooplankton and fish on the bank. The time-dependent anticyclonic circulation around Western Bank was variable, and particle retention rates were 18 and 33% for 20 days at 12.5 and 28.5 m, respectively. The population model showed that both C. typicus and Pseudocalanus spp. are capable of increasing their population size despite advective loss and mortality rates approaching 10%·day-1. We conclude that local production exceeding advective loss rates can explain the high concentrations of zooplankton on Western Bank.
Thermal heterogeneity, stream channel morphology, and salmonid abundance in northeastern Oregon streams
Authors: Ebersole Joseph L , Liss William J , Frissell Christopher A
Published: November 2003

Heterogeneity in stream water temperatures created by local influx of cooler subsurface waters into geomorphically complex stream channels was associated with increased abundance of rainbow trout (Oncorhynchus mykiss) and chinook salmon (Oncorhynchus tshawytscha) in northeastern Oregon. The addition of cold water patch frequency and area as explanatory variables in salmonid habitat models indicated that doubling of cold water patch frequency was associated with increases in rainbow trout and chinook salmon abundances of 31% and 59%, respectively. Doubling of cold water patch area was associated with changes of 10% in rainbow trout abundance but was not associated with chinook abundance after accounting for other habitat factors. The physiognomy, distribution, and connectivity of cold water patches, important attributes determining the effectiveness of these habitats as thermal refuges for stream fishes, were associated with channel bedform and riparian features. Monitoring of thermal heterogeneity and salmonid populations in response to ongoing habitat restoration efforts will provide additional insights into causal relationships among these factors.
Cognitive Function, Fatigue, and Menopausal Symptoms in Women Receiving Adjuvant Chemotherapy for Breast Cancer
Authors: Tchen Nadine , Juffs Helen G. , Downie Fiona P. , Yi Qi-Long , Hu Hanxian , Chemerynsky Irene , Clemons Mark , Crump Michael , Goss Paul E. , Warr David , Tweedale Mary E. , Tannock Ian F.
Published: November 2003

Purpose: There is evidence that cognitive dysfunction, fatigue, and menopausal symptoms may occur in women receiving adjuvant chemotherapy for breast cancer. Here, we determine their incidence and severity, and interrelationships between them and quality of life.

Patients and Methods: In this study, 110 women receiving adjuvant chemotherapy each nominated a female relative, friend, or neighbor (matched by age) as a control; 100 eligible matched pairs were evaluated. Patients and controls completed the following assessments: the High-Sensitivity Cognitive Screen, and the Functional Assessment of Cancer Therapy–General (FACT-G) quality of life scale with subscales for fatigue (FACT-F) and endocrine symptoms (FACT-ES). They also performed tests of attention and reaction time.

Results: Patients and controls were well matched for age and level of education. There was a higher incidence of moderate or severe cognitive impairment in the patient group (16% v 4%; P = .008). Patients experienced much more fatigue than controls (median FACT-F scores, 31 v 46; P < .0001) and more menopausal symptoms (median FACT-ES scores, 58 v 64; P < .0001). Self-reported quality of life of the patients was poorer than for controls, especially in physical and functional domains (median FACT-G scores, 77 v 93; P < .0001). There was strong correlation between fatigue, menopausal symptoms, and quality of life (P < .0001 for each pair), but none were significantly associated with the presence of cognitive dysfunction.

Conclusion: Adjuvant chemotherapy causes cognitive dysfunction, fatigue, and menopausal symptoms in women with breast cancer. Priority should be given to the study of strategies that might reduce these toxic effects.
Differences in Treatment and Outcome Between African-American and White Women With Endometrial Cancer
Authors: Randall Thomas C. , Armstrong Katrina
Published: November 2003

Purpose: To investigate disparities in treatment and outcomes between African-American and white women with endometrial cancer.

Patients and Methods: We analyzed 1992 to 1998 Surveillance, Epidemiology, and End Results data for 21,561 women with epithelial cancers of the endometrium. Sequential Cox proportional hazard models were used to determine the association between tumor characteristics (stage, grade, and histologic type), sociodemographic characteristics (age and marital status), and treatment (surgery and radiation therapy) and the racial difference in mortality.

Results: The unadjusted hazard ratio (HR) for death from endometrial cancer for African-American women compared with white women was 2.57. However, African-American women were significantly more likely to present with advanced-stage disease and have poorly differentiated tumors or tumors with an unfavorable histologic type and were significantly less likely to undergo definitive surgery at all stages of disease. Adjusting for tumor and sociodemographic characteristics lowered the HR for African-American women to 1.80. Further adjustment for the use of surgery reduced the HR to 1.51. The association between surgery and survival was stronger among white women (HR, 0.26) than among African-American women (HR, 0.44).

Conclusion: African-American women with endometrial cancer are significantly less likely to undergo primary surgery and have significantly shorter survival than white women with endometrial cancer. Racial differences in treatment are associated with racial differences in survival. The association between use of surgery and survival is weaker among African-American than white women, raising questions about potential racial differences in the effectiveness of surgery.
Prospective Multicenter Validation Confirms the Prognostic Superiority of the Endometrial Carcinoma Prognostic Index in International Federation of Gynecology and Obstetrics Stage 1 and 2 Endometrial Carcinoma
Authors: Baak Jan P.A. , Snijders Wim , van Diermen Bianca , van Diest Paul J. , Diepenhorst Fred W. , Benraadt Jantine
Published: November 2003

Purpose: To validate the prognostic value of the endometrial carcinoma prognostic index (ECPI; combined myometrium invasion, flow cytometric DNA ploidy, and morphometric mean shortest nuclear axis [MSNA]) versus classic prognosticators.

Patients and Methods: Prospective multicenter ECPI analysis was conducted in 463 endometrial carcinomas with a median of 6.5 years (range, 1 to 10 years) follow-up, review of pathology features, and univariate (Kaplan-Meier) and multivariate (Cox) analyses.

Results: Initial routine and review diagnoses varied considerably (invasion depth, 11%; type, 20%; grade, 34%; vessel invasion, 72%); the review diagnoses were stronger prognostically. In International Federation of Gynecology and Obstetrics stage 1 (after histopathologic examination; pFIGO-1; n = 372; 38 deaths occurred as a result of disease [10.2%]), DNA ploidy was prognostic in hysterectomies (P < .00001) but not in curettages (P = .06). ECPI was a stronger prognostic indicator than other features. ECPI, MSNA, and DNA ploidy were also prognostic in pFIGO-1B and -1C subgroups. Multivariate analysis in pFIGO-1 showed that uterine MSNA ≤ versus > 7.93 μm (hazard ratio [HR], 3.4) and grade (as 1 + 2 v 3; HR, 2.6) added to the ECPI (HR, 32), but only in patients with an unfavorable ECPI of > 0.87. Adjuvant radiotherapy was not an independent prognostic factor in any of the subgroups. In pFIGO-2 (n = 46), ECPI, DNA-ploidy, and age (≤ 64, > 64 years) were significant. In FIGO-3 (n = 31) and FIGO-4 (n = 14), none of the classic or other features analyzed was of prognostic value, which explains why in previous studies using different mixtures of FIGO stages, DNA ploidy prognostic results varied.

Conclusion: In endometrial carcinoma, DNA-ploidy is prognostic in hysterectomy and not in curettage samples. The ECPI is prognostically much stronger than the classic features widely used for therapy triage in pFIGO-1 and -2.
Analgesic Effect of Auricular Acupuncture for Cancer Pain: A Randomized, Blinded, Controlled Trial
Authors: Alimi David , Rubino Carole , Pichard-Léandri Evelyne , Fermand-Brulé Sabine , Dubreuil-Lemaire Marie-Laure , Hill Catherine
Published: November 2003

Purpose: During the last 30 years, auricular acupuncture has been used as complementary treatment of cancer pain when analgesic drugs do not suffice. The purpose of this study is to examine the efficacy of auricular acupuncture in decreasing pain intensity in cancer patients.

Patients and Methods: Ninety patients were randomly divided in three groups; one group received two courses of auricular acupuncture at points where an electrodermal signal had been detected, and two placebo groups received auricular acupuncture at points with no electrodermal signal (placebo points) and one with auricular seeds fixed at placebo points. Patients had to be in pain, attaining a visual analog score (VAS) of 30 mm or more after having received analgesic treatment adapted to both intensity and type of pain, for at least 1 month of therapy. Treatment efficacy was based on the absolute decrease in pain intensity measured 2 months after randomization using the VAS.

Results: The main outcome was pain assessed at 2 months, with the assessment at 1 month carried over to 2 months for the eight patients who interrupted treatment after 1 month. For three patients, no data were available because they withdrew from the study during the first month. Pain intensity decreased by 36% at 2 months from baseline in the group receiving acupuncture; there was little change for patients receiving placebo (2%). The difference between groups was statistically significant (P < .0001).

Conclusion: The observed reduction in pain intensity measured on the VAS represents a clear benefit from auricular acupuncture for these cancer patients who are in pain, despite stable analgesic treatment.
Neuroblastoma Mass Screening in Late Infancy: Insights Into the Biology of Neuroblastic Tumors
Authors: Kerbl Reinhold , Urban Christian E. , Ambros Inge M. , Dornbusch Hans J. , Schwinger Wolfgang , Lackner Herwig , Ladenstein R. , Strenger V. , Gadner H. , Ambros Peter F.
Published: November 2003

Purpose: Neuroblastoma screening in early infancy has detected predominantly “favorable” tumors. We postponed screening to an age between 7 and 12 months to test whether this shift of screening age might influence the detection rate of genetically/clinically unfavorable tumors.

Patients and Methods: In a 10-year period, 313,860 infants were screened by analysis of urine catecholamines. When a neuroblastoma was diagnosed, at least two different areas from every tumor were analyzed for genetic features (MYCN amplification, 1p status, ploidy). Furthermore, neuroblastoma incidence and mortality of the screened group and the cohort of 572,483 children not participating in the screening program were compared.

Results: Forty-six neuroblastomas were detected by mass screening. In 17 tumors (37%) at least one of the biologic features was “unfavorable.” In 10 of 17 patients, one or more of these alterations were only focally present (tumor heterogeneity). In the screened cohort, neuroblastoma incidence was significantly higher when compared with unscreened children (18.2 v 11.2/100,000 births), while there was a trend towards lower incidence of stage 4 over 1 year (2.2 v 3.8). Mortality was not significantly different (0.96 v 1.57).

Conclusion: In contrast to other neuroblastoma screening programs, more than one-third of patients were found with unfavorable genetic markers in our study. The high proportion of focal alterations suggests that biologically young neuroblastomas may consist of genetically favorable and unfavorable parts/areas/clones. We conclude that at least one-third of neuroblastomas detected by screening in late infancy are anticipated cases. This, however, does not result in significantly reduced mortality.
Purification and characterization of tannin acyl hydrolase from Aspergillus niger MTCC 2425
Authors: Bhardwaj Rita , Singh Birbal , Bhat Tej K.
Published: November 2003

The present investigation was carried out for increasing the yield of tannase of Aspergillus niger and the physico‐chemical characterization of this enzyme. Homogenization and detergent pretreatments did not have any remarkable effect on the extraction of enzyme protein. However, extraction of fungal pigments and proteins was observed to have high pH dependence, and maximum enzyme extraction was obtained at pH 5.5. The two‐step purification protocol gave 51‐fold purified enzyme with a yield of 20%. The total tannase activity was made up of nearly equal activity of esterase and depsidase. Sodium dodecyl sulphate‐polyacrylamide gel electrophoresis of purified tannase protein indicated it to be made up of two polypeptides of molecular weight 102 and 83 kDa. Based on the Michaelis‐Menten constant (Km) of tannase for three substrates tested, tannic acid was the best substrate with Km of 2.8 × 10−4 M, followed by methyl gallate and propyl gallate. The inhibition was maximum for CaCl2 (58%) whereas EDTA had no modulatory effect on tannase activity. The inhibitor binding constant (KI) of CaCl2 was 5.9 × 10−4 M and the inhibition was of noncompetitive type.
Effect of prostaglandin A1 in porcine cells persistently infected with classical swine fever virus
Authors: Pereira Freitas Tânia Rosária , Caldas Lúcio Ayres , Rebello Moacyr Alcoforado
Published: November 2003

Cyclopentenone prostaglandins are potent inhibitors of a wide variety of RNA and DNA viruses. In this report we describe that prostaglandin A1 (PGA1) potently inhibited the replication of classical swine fever virus in cultures of PK‐15 cells. The highest non‐toxic dose (5 μg/ml) inhibited virus yield in 99% at the initial phase of infection and in 77% in persistent infected cells. However when PGA1 was removed from persistently infected cells, the inhibition of virus replication was partially reverted.
Influence of carbon source on pyrimidine synthesis in Pseudomonas mendocina
Authors: Santiago Manuel F. , West Thomas P.
Published: November 2003

The effect of carbon source on the regulation of the de novo pyrimidine biosynthetic enzymes in the bacterium Pseudomonas mendocina was studied. When glucose was the carbon source, orotic acid supplementation of P. mendocina cells produced the greatest depression of aspartate transcarbamoylase, dihydroorotate dehydrogenase and orotate phosphoribosyltransferase activities while P. mendocina cells grown in the presence of uracil caused the maximal decrease in dihydroorotase and OMP decarboxylase activities. After the pyrimidine starvation of an orotate phosphoribosyltransferase mutant strain of P. mendocina grown on glucose, the pyrimidine biosynthetic pathway enzyme activities were generally diminished. With respect to pyrimidine starvation studies, the carbon source glucose appeared to lessen regulation at the level of enzyme synthesis compared to what has been observed when succinate served as the carbon source. The regulation of the pyrimidine biosynthetic pathway by carbon source in P. mendocina appeared to differ from how carbon source influenced the control of pyrimidine biosynthesis in the closely‐related species Pseudomonas stutzeri.
Epigenetic change: new from the seeds of the old
Authors: Burt George
Published: November 2003

This paper argues against the division of the perception of change into two dominant forms in the strategic change literature, incremental and paradigmatic. It argues that rather than the either/or nature of the incremental and paradigmatic change interpretation, there is a continuum of levels of real world change, with every change being capable of being interpreted as incremental at one aspirational level and paradigmatic at another.

The paper argues for a new type of change, termed ‘epigenetic change’. Epigenesis is the organic formation of new cells from existing cells. Epigenetic change is therefore partly within and partly outside recipe change. Epigenesis implies discontinuity, but where the old contains the seed of the new. It is argued that change can take place at three levels: incremental change, epigenetic change and paradigmatic change.

Copyright © 2003 John Wiley & Sons, Ltd.
Proteomics and regulomics: The yin and yang of functional genomics
Authors: Werner Thomas
Published: November 2003

I.
Introduction
25

A.  A Brief History of Computer Application in Protein Sequence Analysis
25

B.  Requirements of Current Proteomics Research
26

C.  Mass Spectrometry Applications in Proteomics
26

   II.
Basics of Transcriptional Regulation
26

A.  How Is Transcriptional Coregulation Achieved?
26

B.  Promoters and Transcription Complexes
27

  III.
Synergisms Between Gene Regulation and Mass Spectrometry‐Based Proteomics
29

A.  Expression Array‐Based Gene Selection
29

B.  Protein Data‐Driven Coregulation Analysis
30

C.  A Practical Application Example
30

  IV.
Conclusions
30

Acknowledgments
32

References
32

Protein analysis is a field of research with a long history. Recently, the development of a series of proteomics approaches, i.e., simultaneous analyses on all or a majority of proteins in a cell at a given state, has reinvigorated protein analyses. Mass Spectrometry also developed into one of the most versatile technical tools supporting or even enabling many proteomics‐oriented approaches, providing a convenient link between experimental protein analysis and the corresponding amino acid sequences. Thus direct links to the genomic sequence can be established, which opens the door for a synergistic combination with genomic sequence analysis. This review focuses especially on aspects of genome‐wide transcription control, regulomics in analogy to all the other ‐omics, and how a combination of MS‐based proteomics with in silico regulomics analyses can produce synergistic effects in the quest to understand how cells function. This is illustrated on a real life example showing how the MS‐analysis and in silico promoter analysis can extend the list of candidates for signaling pathways, here the MAP kinase pathway. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 23:25–33, 2004
Environmental and food applications of LC–tandem mass spectrometry in pesticide‐residue analysis: An overview
Authors: Picó Yolanda , Blasco Cristina , Font Guillermina
Published: November 2003

I.
Introduction
45

   II.
Pesticide Structures and Properties
46

  III.
Extraction and Isolation Methods from Environmental and Food Samples
47

  IV.
LC/MS/MS Analysis of Pesticides
53

A.  Interfacing Systems
53

B.  Instrumental Aspects
57

C.  Optimization of Chromatographic Mass Spectrometric Conditions
57

    V.
Tandem MS Methods
59

A.  Triple Quadrupole
59

B.  Quadrupole Ion Trap
66

C.  Hybrid Quadrupole TOF (Q‐TOF)
71

    VI.
Performance Characteristics of LC‐Tandem MS for Pesticides
72

   VII.
Applications
75

  VIII.
Conclusions
80

References
81

An overview is given on pesticide‐residue determination in environmental and food samples by liquid chromatography/mass spectrometry/mass spectrometry (LC/MS/MS). Pesticides comprise a large number of substances that belong to many completely different chemical groups, the only common characteristic is that they are effective against pests. They still constitute a challenge in MS because there is no collective pathway for fragmentation. A brief introduction to the theory of tandem MS permits a discussion of which parameters influence the ionization efficiency when the ions are subjected to different actions. Emphasis is placed on the different tandem MS instruments: triple and ion‐trap quadrupoles, and hybrid quadrupole time‐of‐flight (Q‐TOF), including advantages and drawbacks, typical detection limits, and ion signals at low concentrations. The instrumental setup, as well as LC and mass spectrometric experimental conditions, must be carefully selected to increase the performance of the analytical system. The capacity of each instrument to provide useful data for the identification of pesticides, and the possibility to obtain structural information for the identification of target and non‐target compounds, are discussed. Finally, sample preparation techniques and examples of applications are debated to reveal the potential of the current state‐of‐the‐art technology, and to further promote the usefulness of tandem MS. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 23:45–85, 2004
An approach to remove albumin for the proteomic analysis of low abundance biomarkers in human serum
Authors: Ahmed Nuzhat , Barker Gillian , Oliva Karen , Garfin David , Talmadge Kenneth , Georgiou Harry , Quinn Michael , Rice Greg
Published: November 2003

Proteomic technologies are being used to discover and identify disease‐associated biomarkers. The application of these technologies in the search for potential diagnostic/prognostic biomarkers in the serum of patients has been limited by the presence of highly abundant albumin and immunoglobulins that constitute approximately 60–97% of the total serum proteins. The purpose of the study was to evaluate whether treatment of human serum with Affi‐Gel Blue alone or in combination with Protein A (Aurum serum protein mini kit, Bio‐Rad) before two‐dimensional gel electrophoresis (2‐DE) analysis removed high abundance proteins to allow the visualization of low abundant proteins. Serum samples were treated with either Affi‐Gel Blue or Aurum kit and then subjected to 2‐DE using 11 cm, pH 4–7 isoelectric focussing strips for the first dimension and 10% sodium dodecyl sulfate‐polyacrylamide gel electrophoresis for second dimension. Protein spots were visualized using a fluorescent protein dye (SYPRO Ruby, Bio‐Rad). Comparison between treatment methods showed significant removal of albumin by both Affi‐Gel Blue and Aurum kit and considerable differences in the protein profile of the gels after each treatment. Direct comparison between treatments revealed twenty‐eight protein spots unique to Affi‐Gel Blue while only two spots were unique after Aurum kit treatment. Unique spots in Affi‐Gel Blue and Aurum kit treated serum were not visualized in untreated serum. Sixteen hours of Affi‐Gel Blue treatment resulted in enhanced visualization of fifty‐three protein spots by two‐fold, thirty‐one by five‐fold, twelve by ten‐fold and six by twenty‐fold. In parallel after Aurum kit treatment two‐, five‐, ten‐ and twenty‐fold enhancements of thirty, thirteen, eight and five protein spots, respectively, were observed. The pattern of increased visualization of protein spots with both treatment methods was similar. In conclusion, treatment of serum samples with Affi‐Gel Blue or Aurum kit before 2‐DE analysis can be used to remove high abundance proteins in order to increase the detection sensitivity of proteins present in low abundance.
Analysis of the activity and identification of enzymes after separation of cytosol proteins in mouse liver by microscale nondenaturing two‐dimensional electrophoresis
Authors: Shimazaki Youji , Sugawara Yuki , Ohtsuka Yuki , Manabe Takashi
Published: November 2003

Enzyme activities such as of fructose bisphosphatase, malate dehydrogenase and carbonic anhydrase were analyzed after cytosol proteins in the mouse liver and were separated using nondenaturing two‐dimensional electrophoresis (2‐DE). The activities of both fructose bisphosphatase and malate dehydrogenase were inhibited by thyroxine, and fructose bisphosphatase activity was specifically inhibited by adenosine monophosphate in nondenaturing 2‐DE. Furthermore, polypeptides of the separated proteins were analyzed by peptide mass fingerprinting using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry or by peptide sequencing using electrospray ionization‐tandem mass spectrometry, or both. Proteins separated by 2‐DE were identified. These results indicate that the function of proteins such as enzyme activity, and their sequence structure can be analyzed, for example by peptide mapping and peptide sequencing, after the proteins have been separated by nondenaturing 2‐DE. Present results also indicate analysis of enzyme activity using nondenaturing 2‐DE can be applied to screen substances which affect enzyme activity.
Profiling of the cell surface proteome
Authors: Jang Jun Ho , Hanash Samir
Published: November 2003

The in depth‐mining of the proteome necessitates the comprehensive analysis of proteins in individual subcellular compartments to uncover interesting patterns of protein expression that include assessment of protein location, trafficking and of post‐translational modifications that are location specific. One of the compartments of substantial interest from a diagnostic and therapeutic point of view is the plasma membrane which contains intrinsic membrane proteins and other proteins expressed on the cell surface. Technologies are currently available for the comprehensive profiling of the cell surface proteome that rely on protein tagging of intact cells. Studies are emerging that point to unexpected patterns of expression of specific proteins on the cell surface, with a common occurrence of proteins previously considered to occur predominantly in other compartments, notably the endoplasmic reticulum. The profiling of the cell surface and plasma membrane proteomes will likely provide novel insights and uncover disease related alterations.
Antibody‐dependent enhancement of viral infection: molecular mechanisms and in vivo implications
Authors: Takada Ayato , Kawaoka Yoshihiro
Published: November 2003

Besides the common receptor/coreceptor‐dependent mechanism of cellular attachment, some viruses rely on antiviral antibodies for their efficient entry into target cells. This mechanism, known as antibody‐dependent enhancement (ADE) of viral infection, depends on the cross‐linking of complexes of virus–antibody or virus–activated complement components through interaction with cellular molecules such as Fc receptors or complement receptors, leading to enhanced infection of susceptible cells. Recent studies have suggested that additional mechanisms underlie ADE: involvement of complement component C1q and its receptor (Ebola virus), antibody‐mediated modulation of the interaction between viral protein and its coreceptor (human immunodeficiency virus) and suppression of cellular antiviral genes by the replication of viruses entering cells via ADE (Ross River virus). Since ADE is exploited by a variety of viruses and has been associated with disease exacerbation, it may have broad relevance to the pathogenesis of viral infection and antiviral strategies. Copyright © 2003 John Wiley & Sons, Ltd.
The legacy of C. West Churchman: a framework for social systems assessments
Authors: Nelson Harold G.
Published: November 2003

This paper is an overview of a framework for social systems assessment based on my study and work with C. West Churchman. The framework is an outgrowth of the systems categories developed by Churchman as part of his definition of teleological systems. It is an expansion of the methodologies used for socio‐economic impact assessments that has evolved out of the value distribution assessment process first used in my graduate studies of the impact of geothermal energy development on rural communities in northern California. This social systems assessment framework is inclusive of social systems analysis, social systems intervention and social systems redesign and provides an organizing structure for relating the diverse theories, methods and experiences of systems scholars and practitioners. This framework is part of the rich legacy of systems approaches that continue to be developed from the seminal work of C. West Churchman. Copyright © 2003 John Wiley & Sons, Ltd.
Efficacy of azithromycin for the treatment of feline chlamydophilosis
Authors: Owen WMA , Sturgess CP , Harbour DA , Egan K , Gruffydd-Jones T.J.
Published: November 2003

The current recommended treatment for feline chlamydophilosis involves daily oral administration of antimicrobials to all cats within an affected group for a prolonged period of time (4–6 weeks). Not surprisingly, owner compliance can be poor resulting in apparent treatment failure. Recent anecdotal evidence, supported by its efficacy in the treatment of Chlamydia trachomatis infection in humans, has suggested that azithromycin may offer an alternative by allowing less frequent dosing for a shorter duration. A clinical trial was designed to evaluate the efficacy of azithromycin for the treatment of chlamydia ( Chlamydophila felis) infection in cats. Whilst azithromycin, given at 10–15 mg/kg daily for 3 days and then twice weekly, provided a similar, rapid resolution of clinical signs and negative isolation scores as doxycycline, C felis was re-isolated in four out of the five cats treated. Furthermore, even daily administration of azithromycin to chronically infected cats was ineffective in clearing infection. The azithromycin protocols used here were therefore found to be unsuccessful in eliminating the carriage of this strain of C felis.
Impact of clouds and aerosols on photolysis frequencies and photochemistry during TRACE‐P: 1. Analysis using radiative transfer and photochemical box models
Authors: Lefer B. L. , Shetter R. E. , Hall S. R. , Crawford J. H. , Olson J. R.
Published: November 2003

This study examines the agreement between photolysis frequency measurements by the NCAR scanning actinic flux spectroradiometer (SAFS) and calculations from a cloud‐free model (CFM) and investigates the impact of these differences on ozone photochemistry. Overall, the mean jNO2measurement to model ratio for all flights of TRACE‐P was 0.943 ± 0.271. The sky conditions during the Transport and Chemical Evolution over the Pacific (TRACE‐P) experiment were determined to be “cloud‐free” 40% of the time; hence a CFM is frequently not representative of the local atmospheric conditions. Our analysis indicates that clouds have a larger impact on photolysis frequencies (from −90 to +200%) than do aerosols (maximum of ±20%). The CFM and SAFS jNO2 and jO(1D) values differed by 9% and 0–7%, respectively, during a vertical profile through a cloud‐free and low AOD atmosphere. This suggests that measurement/model agreement to less than 10% may be difficult without better aerosol optical parameter inputs even under low‐AOD conditions. For the TRACE‐P chemical environment, OH, NO, and HO2 were more sensitive than other compounds (e.g., CH3C(O)O2, CH3OOH) to changes (or errors) in photolysis frequency inputs to a photochemical box model. Compounds including NO2, PAN, and HCHO exhibited different relationships to j‐value changes below and above the boundary layer. Ozone production and loss rates increased linearly with changes (or errors) in the photolysis frequency with the resulting net O3 tendency increasing with a linear slope near unity. During the TRACE‐P mission the net photochemical effect of clouds and aerosols was a large decrease in photochemical O3 production in the boundary layer.
Contribution of biomass and biofuel emissions to trace gas distributions in Asia during the TRACE‐P experiment
Authors: Woo Jung‐Hun , Streets David G. , Carmichael Gregory R. , Tang Youhua , Yoo Bongin , Lee Won‐Chan , Thongboonchoo Narisara , Pinnock Simon , Kurata Gakuji , Uno Itsushi , Fu Qingyan , Vay Stephanie , Sachse Glen W. , Blake Donald R. , Fried Alan , Thornton Donald C.
Published: November 2003

A comprehensive emission inventory with enhanced spatial and temporal resolution is used to help quantify the contribution from three source categories (fossil, biofuel, and biomass burning) during the NASA TRACE‐P experiment. Daily biomass burning emissions are developed to support this analysis. Emissions of 27 species and their ratios, by sector, region, and source category are presented. The emission distributions and chemical composition are further analyzed using various statistical techniques. Using cluster analysis, the 27 chemical species are combined into 8 groups that have similar regional distribution, and 52 regions are assembled into 11 regional groups that have similar chemical composition. These groups are used in Chemical Mass Balance analysis to characterize air masses and to quantify the contribution of the three source categories to the observed species distributions. Five DC8 flights with 16 flight segments associated with outflow events are analyzed. In general, Asian outflow is a complex mixture of biofuel, biomass, and fossil sources. Flights in the post frontal regions at high latitudes and low altitudes have a high contribution of fossil fuel emissions. Flights in the warm sector of cold fronts are dominated by biomass burning contributions (about 70%). Biofuel contributions are high (about 70%) when air masses come from central China. The receptor model results are shown to be consistent with other 3‐D chemical model sensitivity studies and analysis using ratios of indicator species (e.g., dK+/dSO42−, CH3CN/SOy, SOy/CO, and C2Cl4/CO).
An assessment of western North Pacific ozone photochemistry based on springtime observations from NASA's PEM‐West B (1994) and TRACE‐P (2001) field studies
Authors: Davis D. D. , Chen G. , Crawford J. H. , Liu S. , Tan D. , Sandholm S. T. , Jing P. , Cunnold D. M. , DiNunno B. , Browell E. V. , Grant W. B. , Fenn M. A. , Anderson B. E. , Barrick J. D. , Sachse G. W. , Vay S. A. , Hudgins C. H. , Avery M. A. , Lefer B. , Shetter R. E. , Heikes B. G. , Blake D. R. , Blake N. , Kondo Y. , Oltmans S.
Published: November 2003

The current study provides a comparison of the photochemical environments for two NASA field studies focused on the western North Pacific (PEM‐West‐B (PWB) and TRACE‐P (TP)). These two studies were separated in calendar time by approximately 7 years. Both studies were carried out under springtime conditions, with PWB being launched in 1994 and TP being deployed in 2001 (i.e., 23 February–15 March 1994 and 10 March–15 April 2001, respectively). Because of the 7‐year time separation, these two studies presented a unique scientific opportunity to assess whether evidence could be found to support the Department of Energy's projections in 1997 that increases in anthropogenic emissions from East Asia could reach 5%/yr. Such projections would lead one to the conclusion that a significant shift in the atmospheric photochemical properties of the western North Pacific would occur. To the contrary, the findings from this study support the most recent emission inventory data [Streets et al., 2003] in that they show no significant systematic trend involving increases in any O3 precursor species and no evidence for a significant shift in the level of photochemical activity over the western North Pacific. This conclusion was reached in spite of there being real differences in the concentration levels of some species as well as differences in photochemical activity between PWB and TP. However, nearly all of these differences were shown to be a result of a near 3‐week shift in TP's sampling window relative to PWB, thus placing it later in the spring season. The photochemical enhancements seen during TP were most noticeable for latitudes in the range of 25–45°N. Most important among these were increases in J(O1D), OH, and HO2 and values for photochemical ozone formation and destruction, all of which were typically two times larger than those calculated for PWB. A comparison of these airborne results with ozonesonde data from four Japanese stations provided further evidence showing that the 3‐week shift in the respective sampling windows of PWB and TP was a likely cause for the differences seen in O3 levels and in photochemical activity between the two airborne studies.
A kinetic approach to the Ponderomotive Force
Authors: Dasgupta B. , Tsurutani B. T. , Janaki M. S.
Published: November 2003

It has been suggested that Magnetic Holes (MHs) are caused by perpendicular proton energization due to the Ponderomotive Force (PF) associated with phase steepened Alfvén waves. Here we include particle finite Larmor radius (FLR) effects and the effects of ion gyroharmonics in the PF expression. The general expression for the PF is derived by using the hot plasma dielectric tensor from kinetic theory. The fully kinetic expression has a multiple resonance character which is not revealed in the fluid picture. It will be shown that by including such effects, the expression for the PF will be significantly altered, both at the low frequency and high frequency limit. Also, an explicit analytic expression for the PF keeping only the first order FLR terms is given for conceptual purposes for the readers.