bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACTSalmonella 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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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).
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

AbstractThe 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

AbstractCyclopentenone 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

AbstractThe 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

Abstract

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

Abstract

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

Abstract

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