bluuebunny/crossref_metadata_2025 huggingface dataset:
Overexpression of the VAV proto‐oncogene product is associated with B‐cell chronic lymphocytic leukaemia displaying loss on 13q
Authors: Prieto‐Sánchez Rosario M. , Hernández José A. , García Juan L. , Gutiérrez Norma C. , Miguel Jesús San , Bustelo Xosé R. , Hernández Jesús M.
Published: April 2006

The expression of the VAV proto‐oncogene in 57 patients with chronic myeloproliferative disease (CMD), B‐cell acute lymphoblastic leukaemia (B‐ALL) and B‐cell non‐Hodgkin Lymphoma (B‐NHL), and 61 with B‐cell chronic lymphocytic leukaemia (B‐CLL) was analysed. VAV overexpression was observed in 19·5% of cases and 81% of VAV‐positive tumours also displayed VAV phosphorylation. Overexpression was not observed in B‐ALL or CMD, but 13% of B‐NHL and 34·4% of B‐CLL patients (P = 0·002) overexpressed VAV. The overexpression and phosphorylation of VAV was detected more frequently in 13q‐ chronic lymphocytic leukaemias (71.4%) versus other B‐CLLs (23·4%, P = 0·001). Overexpression of VAV protein is a frequent event in patients with B‐CLL displaying loss of 13q sequences.
Clathrin anchors deubiquitinating enzymes, AMSH and AMSH‐like protein, on early endosomes
Authors: Nakamura Michihiko , Tanaka Nobuyuki , Kitamura Naomi , Komada Masayuki
Published: April 2006

Endosomal sorting of ubiquitinated membrane proteins for trafficking to lysosomes is executed by a complex of two ubiquitin‐binding proteins, Hrs and STAM, that localizes on a microdomain of early endosomes with a flat clathrin coat. AMSH is a deubiquitinating enzyme that interacts with STAM and is implicated in the down‐regulation of epidermal growth factor receptor. AMSH has a close homolog, AMSH‐like protein (AMSH‐LP). Here we show that AMSH‐LP is also a deubiquitinating enzyme that acts on early endosomes. We further show that AMSH and AMSH‐LP bind to the terminal domain of clathrin heavy chain via a novel clathrin‐binding site conserved between these proteins. Exogenously expressed AMSH and AMSH‐LP co‐localized with clathrin on early endosomes. However, deletion of the clathrin‐binding site from the proteins, as well as RNA interference‐mediated depletion of clathrin heavy chain, resulted in a failure of AMSH and AMSH‐LP to localize on endosomes. In contrast, a mutant of AMSH that lacks the ability to bind STAM localized normally on endosomes. We suggest that AMSH and AMSH‐LP are anchored on the early endosomal membrane via interaction with the clathrin coat.
Immunodetection of GLUT1, p63 and phospho‐histone H1 in invasive head and neck squamous carcinoma: correlation of immunohistochemical staining patterns with keratinization
Authors: Burstein D E , Nagi C , Kohtz D S , Lee L , Wang B
Published: April 2006

Aims : To examine invasive head and neck squamous carcinomas for expression of GLUT1, a glucose transporter and marker of increased glucose uptake, glycolytic metabolism and response to tissue hypoxia; p63, a p53 homologue that is a marker of the undifferentiated proliferative basaloid phenotype; and phospho‐histone H1, a marker of activation of the cell cycle‐promoting cyclin‐dependent kinases 1 and 2.

Methods : Routinely processed slides from 34 invasive squamous carcinomas, including 25 with intraepithelial components, were immunostained with anti‐GLUT1 (Chemicon), anti‐p63 (4A4, Santa Cruz), and antiphospho‐histone H1 (monoclonal 12D11).

Results : In keratinizing carcinomas, all three markers were most commonly immunodetected peripherally, with loss of expression in central keratinized zones. In contrast, in non‐keratinizing carcinomas, p63 and phospho‐histone H1 expression was most commonly observed throughout tumour nests and anti‐GLUT1 stained in a pattern suggestive of hypoxia‐induced expression (‘antistromal’ staining), in which cells at the tumour–stromal interface were GLUT1– and cells in central, perinecrotic zones showed progressive induction of GLUT1. Intraepithelial components also displayed basal and ‘antibasal’ GLUT1 staining patterns, homologous to the pro‐ and antistromal patterns in invasive carcinoma; basal patterns in intraepithelial lesions appeared to be more predictive of keratinizing invasive carcinoma and antibasal intraepithelial staining more predictive of non‐keratinizing poorly differentiated carcinomas.

Conclusions : Keratinizing and non‐keratinizing squamous carcinomas differ in expression patterns of GLUT1, p63 and phospho‐histone H1. In the former, all three markers were typically suppressed in conjunction with keratinization; in the latter, GLUT1 expression was more likely to occur in a hypoxia‐inducible pattern and expression of p63 and phospho‐histone H1 was unsuppressed. GLUT1 expression patterns in intraepithelial lesions may be predictive of the differentiation status of the associated invasive carcinoma.
The Effects of Disruption of A Kinase Anchoring Protein–Protein Kinase A Association on Protein Kinase A Signalling in Neuroendocrine Melanotroph Cells of Xenopus laevis
Authors: Corstens G. J. H. , Van Boxtel R. , Van Den Hurk M. J. J. , Roubos E. W. , Jenks B. G.
Published: April 2006

The secretory activity of melanotroph cells from Xenopus laevis is regulated by multiple neurotransmitters that act through adenylyl cyclase. Cyclic adenosine monophosphate (cAMP), acting on protein kinase A (PKA), stimulates the frequency of intracellular Ca2+ oscillations and the secretory activity of the melanotroph cell. Anchoring of PKA near target proteins is essential for many PKA‐regulated processes, and the family of A kinase anchoring proteins (AKAPs) is involved in the compartmentalisation of PKA type II (PKA II) regulatory subunits. In the present study, we determined to what degree cAMP signalling in Xenopus melanotrophs depends on compartmentalised PKA II. For this purpose, a membrane‐permeable stearated form of Ht31 (St‐Ht31), which dislodges PKA II from AKAP (thus disrupting PKA II signalling), was used. The effect of St‐Ht31 on both secretion of radiolabelled peptides and intracellular Ca2+ signalling by superfused Xenopus melanotrophs was assessed. St‐Ht31 stimulated secretion but had no effect on Ca2+ signalling. We conclude Xenopus melanotrophs possess a St‐Ht31‐sensitive PKA II that is associated with the exocytosis machinery and, furthermore, that Ca2+ signalling is regulated by an AKAP‐independent signalling system. Moreover, our results support a recent proposal that AKAP participates in regulating PKA activity independently from cAMP.
Real time balanced turbo field echo Cine‐MRI in the analysis of deglutition events and transit times
Authors: KARAÇAY Ş. , AKıN E. , SAYıN M. Ö , BULAKBAŞı N.
Published: April 2006

summary Investigation of swallowing is an important part of oral diagnosis. It usually plays a role in the aetiology of some orofacial deformities and open‐bite as well as in the relapse of treated open‐bite patients. In recent years, the movements of the anatomical structures that participate in deglutition have been investigated by several methods such as cineradiography, electromyography, electropalatography, electromagnetic articulography and ultrasonography. However, all these techniques have various disadvantages. Recently, dynamic magnetic resonance imaging has become available in the evaluation of swallowing function.

In this study we intended to present this new technique to the dental literature and aimed to obtain dynamic images of the deglutition process. We also compared the timing of events in subjects with anterior open‐bite and normal overbite during swallowing 10 mL water.
Changing attitudes to the management of ischaemic stroke between 1997 and 2004: a survey of New Zealand physicians
Authors: Somerfield J. , Barber P. A. , Anderson N. E. , Spriggs D. , Charleston A. , Bennett P.
Published: April 2006

Aim: In 1997, a survey of New Zealand physicians’ opinions on the management of stroke was carried out. Since then, there have been a number of advances in stroke therapy. We have repeated the 1997 survey to assess changes in physicians’ opinions on stroke management.

Methods: A questionnaire was sent to 293 physicians responsible for patients admitted with acute stroke to hospitals throughout New Zealand. It included questions on the management of acute stroke and secondary prevention and was based on the 1997 questionnaire.

Results: Responses were received from 211 physicians of whom 174 (82%) managed patients with an acute stroke. The number of respondents who thought that stroke units were efficacious has increased (57% in 1997 to 89%, P < 0.001). The use of aspirin acutely (P < 0.001) and intravenous tissue plasminogen activator (P = 0.006) has also increased. In 2004, antihypertensive therapy for secondary stroke prevention would be commenced if the blood pressure was 150/90 by 98% of respondents and 140/90 by 70% of respondents. In 2004, a statin would be commenced if the total cholesterol level was 4.0 mmol/L by 56% of respondents and 5.0 mmol/L by 91% of respondents.

Conclusions: This survey has shown important changes in the management of ischaemic stroke over the past 7 years.
Significant exercise‐induced hypoxaemia with equivocal desaturation in patients with chronic obstructive pulmonary disease
Authors: Chuang M.‐L. , Lin I.‐F. , Vintch J. R. E. , Ho B. S.‐J. , Chao S.‐W. , Ker J. J. W.
Published: April 2006

Background: The wide 95% confidence interval for SaO2 measured by pulse oximetry (SPO2) and the inherent characteristics of the oxyhaemoglobin dissociation curve can lead to modest but significant decreases in PaO2 (ΔPaO2 ≥ 5 mmHg) that may be under‐appreciated.

Aim: To avoid missing potentially significant ΔPaO2 by using SPO2, this study establishes a threshold of ΔSPO2 to detect ΔPaO2 by examining the correlation between ΔSPO2 and ΔPaO2.

Methods: We enrolled 29 elderly patients with moderate to severe chronic obstructive pulmonary disease as assessed by lung function testing. Arterial blood gases and SPO2 measurements were carried out during maximal exercise testing. The patients were assigned to groups based on PaO2 measurements: group 1 had PaO2 at peak exercise (PaO2peak) ≥60 mmHg without a ΔPaO2; group 2 had PaO2peak ≥ 60 mmHg with a ΔPaO2; group 3 had PaO2peak < 60 mmHg without a ΔPaO2; and group 4 had PaO2peak < 60 mmHg with a ΔPaO2.

Results: The study population was evenly distributed between groups 1, 2 and 4. However, group 3 did not have any patients enrolled in this study that met group 3 criteria. The sensitivity of pulse oximetry required to detect SaO2 below 90% was 19%. ΔSPO2 of 3% may increase the low sensitivity of SPO2 and was shown by a 92% positive predictive value for ΔPaO2 ≥ 5 mmHg.

Conclusion: This study suggests that important changes in oxygenation may be avoided if using ΔSPO2 rather than absolute values of SPO2 in patients with chronic obstructive pulmonary disease undergoing exercise testing to detect exercise‐induced hypoxaemia.
The End of the Shock of the New
Authors: Lightfoot Geoff , Lilley Simon , Kavanagh Donncha
Published: April 2006

‘Shock’ advertising is the new black and the subject of the reflection in which this article engages. We do this in particular through consideration of the (largely) British high‐street fashion house French Connection’s seemingly endless ‘FCUK’ campaign. The obvious resonance between this abbreviation and perhaps the most popular word in the English language was at the heart of the campaign’s appeal and it continues today through various extensions on both slogans and logos on French Connection’s own goods and indeed those who seek to piggy back upon and/or subvert its market power. It is far from the only example of such ‘shock’ tactics. Whether discussing reproduction in graphic detail with children, joyously dismantling chastity, or merely fucking with fuck, it seems that traditional mores can no longer remain virgin territory, unsullied by rapacious marketing. Our mediated experiences of reaching ‘extremes’, it now appears, are not paralysing, mesmerising, fascinating or inspiring but simply a further prod down the path leading to (gleeful) purchase. In this paper we explore how, via a series of semiotic reversals, the new, the strange, the unfamiliar and the would‐be shocking are rendered banal, and thus thoroughly comprehensible through brand association and the endless re‐iteration of existing works.
Creativity and Repetition
Authors: Slutskaya Natalie
Published: April 2006

In this paper we seek to explore the concept of the ‘new’ through enquiring into the role of the body, thus opening categories that may allow a sensing of the affective ‘new’ in organizing processes. We use various theoretical concepts such as ‘repetition’ and ‘habitual appropriation’ to look at modern dance. We aim to show how the investigation of embodied processes allows us to make links between the old and the new, the creative and the unimaginative, and ultimately may help us to generate an infinite array of creative practices.
Practitioner Review: Bridging the gap between research and clinical practice in pediatric obesity
Authors: Jelalian Elissa , Wember Yana Markov , Bungeroth Heidi , Birmaher Vered
Published: April 2006

Background:  Pediatric obesity is a significant public health concern, with rising prevalence rates in both developed and developing countries. This is of particular significance given that overweight children and adolescents are at increased risk for multiple medical comorbidities, as well as psychosocial and behavioral difficulties. The current review highlights findings from the empirical pediatric obesity treatment literature, with particular attention to diet, physical activity, and behavior interventions. Evaluation and treatment considerations relevant to working with overweight children and adolescents with psychiatric comorbidities are reviewed.

Methods:  Review of the relevant treatment literature, with a focus on randomized clinical trials, was conducted. Recommendations regarding treatment of children and adolescents with psychiatric comorbidities are based on relevant prospective studies of the relationship between weight status and psychological variables and studies with adult populations.

Results:  Well‐established pediatric weight control interventions have been conducted in research settings. These studies provide a starting point, but are limited by homogeneous samples that may exclude participants with psychiatric comorbidities. Practitioners treating obese children and adolescents with psychiatric disorders are encouraged to assess individual, familial, and contextual variables specific to weight (e.g., motivation and existing support to change current eating and physical activity patterns, extent of weight‐related conflict within family, impact of weight on current functioning) in order to prioritize treatment objectives.

Conclusions:  The review concludes with a discussion of current empirical and practical challenges, including explicitly targeting obese children and adolescents with psychiatric concerns and determining appropriateness of pursuing weight control interventions in this population.
Discriminating glacial races of burbot (Lota lota) by means of PCR‐RF‐SSCP (PRS) analysis of the mitochondrial control region
Authors: VAN HOUDT J. K. J. , CLEYN L. DE , PERRETTI A. , VOLCKAERT F. A. M.
Published: April 2006

We used closely related haplotypes of the mitochondrial control region of burbot (Lota lota) (Teleostei; Gadidae) with known sequences to assess the sensitivity of a standardized PRS (PCR‐RF‐SSCP) approach. In total, 537 pairwise comparisons between PRS patterns were evaluated. Only seven mutations did not result in a detectable change that resulted in 11 pairwise comparisons (2%) with indistinguishable haplotypes. The haplotypes that could not be discriminated were always characteristic for a certain assemblage (glacial race). As such, this method provides a reliable alternative to direct sequencing for phylogeographic studies in case intrapopulation diversity is limited.
Tetranucleotide microsatellite loci from the striped dolphin (Stenella coeruleoalba Meyen, 1833)
Authors: MIRIMIN L. , COUGHLAN J. , ROGAN E. , CROSS T. F.
Published: April 2006

Five tetranucleotide microsatellite loci were isolated from the striped dolphin (Stenella coeruleoalba). Characterization of these loci revealed between three and 11 alleles at each locus and observed heterozygosity ranged from 0.192 to 0.775. All sets of primers amplified homologous loci when tested on four related species and showed polymorphisms in most locus–species combinations. A sixth microsatellite, which appeared to be monomorphic in the striped dolphin, was also shown to be polymorphic in three related species.
Visual field defects in prematurely born patients with white matter damage of immaturity: a multiple‐case study
Authors: Jacobson Lena , Flodmark Olof , Martin Lene
Published: April 2006

Purpose:  White matter damage of immaturity may affect visual, motor and cognitive functions. This multiple‐case study presents standardized perimetry results in six teenagers and young adults born prematurely with visual dysfunction due to white matter damage of immaturity of pre‐ or perinatal origin.

Methods:  Six subjects, aged 13–25 years, born at a gestational age of 28–34 weeks, with white matter damage of immaturity documented by MRI, and optic disc appearances documented by fundus photography, were examined with manual and computerized quantitative perimetry.

Results:  All subjects had subnormal visual field (VF) function, although the depth and extension of the VF defects differed between subjects. The inferior VF function was more deviant than the superior in all cases. The concordance between the VF defects detected with the different techniques was good, although the static computerized techniques revealed slightly more abnormality.

Conclusion:  White matter damage of immaturity may affect the VF. The lower VF is often more affected than the upper. The abnormalities can be demonstrated by both manual and computerized perimetry.
Dynamic magnetic resonance sialography as a new diagnostic technique for patients with Sjögren's syndrome
Authors: Morimoto Y , Habu M , Tomoyose T , Ono K , Tanaka T , Yoshioka I , Tominaga K , Yamashita Y , Ansai T , Kito S , Okabe S , Takahashi T , Takehara T , Fukuda J , Inenaga K , Ohba T
Published: April 2006

Objective:  To evaluate the clinical utility of dynamic magnetic resonance (MR) sialographic images as a diagnostic tool for patients with Sjögren's syndrome.

Methods:  The morphological findings and various kinds of functional parameters in volunteers on dynamic MR sialographic images were compared with those in five patients with definite Sjögren's syndrome.

Results:  On the MR sialographs of all five patients with Sjögren's syndrome, the so‐called ‘apple‐tree appearance’ was seen. The difference in two functional parameters using the dynamic MR sialographic data was elucidated between the two groups. The maximum area of the detectable ducts in the group of patients was significantly smaller (P < 0.001) than that in the group of volunteers. The ratio of change in the detectable ducts in the group of patients was significantly lower (P = 0.011) than that in the group of volunteers.

Conclusions:  Our study suggests that dynamic MR sialographic data in addition to MR sialographic images might be useful for the diagnosis of Sjögren's syndrome.
Kick-off
Authors: Vieira Armando
Published: April 2006

Most problems in physics textbooks are highly idealized to keep them analytically manageable. However, in dealing with daily phenomena, some models presented in textbooks are oversimplified. The discrepancy between what students observe and what these models predict may cause frustration or even distrust. On the other hand, it is crucial to develop intuition to discover the relevant parameters as well as appropriate optimizations—a common perspective in engineering that is not always stressed in physics. This paper addresses these topics in a concrete situation: kicking a soccer ball. The problem is formulated as follows: Given the physical constraints of the athlete, how does one achieve maximum initial velocity and range?
Battle of the Merry-Go-Rounds: An Angular Momentum Demonstration
Authors: Van Hook Stephen J.
Published: April 2006

Introducing paradoxes where two concepts appear to conflict is a time-honored method of challenging students to think deeper about the concepts. In The Battle of the Merry-Go-Rounds, two adjacent, interacting merry-go-rounds (MGR) exhibit behavior that leads to an apparent contradiction between two fundamental physics principles. This simple demonstration challenges students to think carefully about angular momentum and the notion of a closed system.
Syntheses of Base and Side-Chain Modified Pyrimidine 1-[2-(Phosphonomethoxy)propyl] Derivatives as Potent Inhibitors of Thymidine Phosphorylase (PD-ECGF) from SD-Lymphoma
Authors: Pomeisl Karel , Votruba Ivan , Holý Antonín , Pohl Radek
Published: April 2006

In this study we synthesized a series of thymine and 5-ethyluracil acyclic nucleoside phosphonates bearing hydroxymethyl, methoxymethyl, azidomethyl, aminomethyl and (trimethylammonio)methyl group in side chain as potent inhibitors of thymidine phosphorylase. In addition, we investigated in particular the novel syntheses of fluorinated derivatives containing fluoromethyl or trifluoromethyl groups in side chain such as 5-ethyl- 1-[(S)-3-fluoro-2-(phosphonomethoxy)propyl]uracil (8) or 5-ethyl-1-[3,3,3-trifluoro-2-(phosphonomethoxy)propyl]uracil and thymine derivatives 27 and 28. Uracil acyclic nucleoside phosphonates 1-{2-[(diisopropoxyphosphoryl)methoxy]ethyl}uracil (12) and 1-{2-[(diisopropoxyphosphoryl)methoxy]-3,3,3-trifluoropropyl}uracil (19) were fluorinated to corresponding 5-fluorouracil derivatives. While the 5-fluorouracil derivatives exhibit a marginal inhibitory effect, thymine and 5-ethyluracil compound with fluorine in side chains possess considerable inhibitory potency toward thymidine phosphorylase from rat spontaneous T-cell lymphoma.
Fluorescent Labels for Aldehydes
Authors: Langhals Heinz , Fuchs Kerstin
Published: April 2006

The fluorescence labeling of aldehydes with perylene bis(dicarboximide)s by the formation of acetals is described.
COMPUTATION OF NEUTRON STAR STRUCTURE USING MODERN EQUATION OF STATE
Authors: BORDBAR G. H. , HAYATI M.
Published: April 2006

Using the modern equations of state derived from microscopic calculations, we have calculated the neutron star structure. For the neutron star, we have obtained a minimum mass about 0.1 M⊙ which is nearly independent of the equation of state, and a maximum mass between 1.47 M⊙ and 1.98 M⊙ which is strongly dependent on the equation of state. It is shown that among the equations of state of neutron star matter which we have used, the stiffest one leads to higher maximum mass and radius and lower central density. It is seen that the given maximum mass for the Reid-93 equation of state shows a good consistency with the accurate observations of radio pulsars. We have indicated that the thickness of neutron star crust is very small compared to the predicted neutron star radius.
Large‐scale stochastic hereditary systems under Markovian structural perturbations. Part III. Qualitative analysis
Authors: Ladde G. S.
Published: April 2006

In this final part of the work, the convergence and stability
analysis of large‐scale stochastic hereditary systems under random
structural perturbations is investigated. This is achieved
through the development and the utilization of comparison theorems
in the context of vector Lyapunov‐like functions and
decomposition‐aggregation method. The byproduct of the
investigation suggests that the qualitative properties of
decoupled stochastic hereditary subsystems under random structural
perturbations are preserved, as long as the self‐inhibitory
effects of subsystems are larger than cross‐interaction effects of
the subsystems. Again, it is shown that these properties are
affected by hereditary and random structural perturbations
effects. It is further shown that the mathematical conditions are
algebraically simple, and are robust to the parametric changes.
Moreover, the work generates a concept of block quasimonotone
nondecreasing property that is useful for the investigation of
hierarchic systems. These results are further extended to the
integrodifferential equations of Fredholm type.
Multivalued H‐essential maps of acyclic type on Hausdorfftopological spaces
Authors: O′Regan Donal
Published: April 2006

This paper discusses acyclic maps between topological spaces. We
show that if F
is H‐essential and F≅G, then G has a
fixed point.
Flow of a Newtonian fluid in a symmetrically heated channel: Effect of viscosity and viscous dissipation
Authors: Adegbie K. S. , Alao F. I.
Published: April 2006

This paper discusses the effect of viscosity and viscous
dissipation (due to a high velocity gradient) on the steady flow
of a viscous liquid in a symmetrically heated channel. The coupled
nonlinear differential equations arising in the planar Poiseuille
flow are not amendable to analytical solutions. Therefore,
numerical solutions based on finite‐difference scheme are
presented. The effects of various flow controlling parameters such
as temperature difference α, dimensionless pressure
gradient, and the dimensionless viscous heating parameter δ on the dimensionless velocity and temperature are analyzed. The
analysis reveals that when viscous heating parameter δ = 0, we obtained zero solution for the dimensionless temperature.
Functional ABCG2 is overexpressed on primary CML CD34+ cells and is inhibited by imatinib mesylate
Authors: Jordanides Niove E. , Jorgensen Heather G. , Holyoake Tessa L. , Mountford Joanne C.
Published: April 2006

Imatinib mesylate (IM) therapy for chronic myeloid leukemia (CML) has transformed the treatment of this disease. However, the vast majority of patients, despite major responses, still harbor Philadelphia chromosome–positive (Ph+) cells. We have described a population of primitive Ph+ cells that are insensitive to IM and may be a source of IM resistance. Cell line studies have suggested that the drug transporter ABCG2 may be a mediator of IM resistance, however there is considerable debate about whether IM is an ABCG2 substrate or inhibitor. We demonstrate here that primitive CML CD34+ cells aberrantly overexpress functional ABCG2 but that cotreatment with IM and an ABCG2 inhibitor does not potentiate the effect of IM. We definitively show that IM is an inhibitor of, but not a substrate for, ABCG2 and that, therefore, ABCG2 does not modulate intracellular concentrations of IM in this clinically relevant cell population.
The PLAC1-homology region of the ZP domain is sufficient for protein polymerisation
Authors: Jovine Luca , Janssen William G , Litscher Eveline S , Wassarman Paul M
Published: April 2006

Background

Hundreds of extracellular proteins polymerise into filaments and matrices by using zona pellucida (ZP) domains. ZP domain proteins perform highly diverse functions, ranging from structural to receptorial, and mutations in their genes are responsible for a number of severe human diseases. Recently, PLAC1, Oosp1-3, Papillote and CG16798 proteins were identified that share sequence homology with the N-terminal half of the ZP domain (ZP-N), but not with its C-terminal half (ZP-C). The functional significance of this partial conservation is unknown.

Results

By exploiting a highly engineered bacterial strain, we expressed in soluble form the PLAC1-homology region of mammalian sperm receptor ZP3 as a fusion to maltose binding protein. Mass spectrometry showed that the 4 conserved Cys residues within the ZP-N moiety of the fusion protein adopt the same disulfide bond connectivity as in full-length native ZP3, indicating that it is correctly folded, and electron microscopy and biochemical analyses revealed that it assembles into filaments.

Conclusion

These findings provide a function for PLAC1-like proteins and, by showing that ZP-N is a biologically active folding unit, prompt a re-evaluation of the architecture of the ZP domain and its polymers. Furthermore, they suggest that ZP-C might play a regulatory role in the assembly of ZP domain protein complexes.
Mining gene expression data by interpreting principal components
Authors: Roden Joseph C , King Brandon W , Trout Diane , Mortazavi Ali , Wold Barbara J , Hart Christopher E
Published: April 2006

Background

There are many methods for analyzing microarray data that group together genes having similar patterns of expression over all conditions tested. However, in many instances the biologically important goal is to identify relatively small sets of genes that share coherent expression across only some conditions, rather than all or most conditions as required in traditional clustering; e.g. genes that are highly up-regulated and/or down-regulated similarly across only a subset of conditions. Equally important is the need to learn which conditions are the decisive ones in forming such gene sets of interest, and how they relate to diverse conditional covariates, such as disease diagnosis or prognosis.

Results

We present a method for automatically identifying such candidate sets of biologically relevant genes using a combination of principal components analysis and information theoretic metrics. To enable easy use of our methods, we have developed a data analysis package that facilitates visualization and subsequent data mining of the independent sources of significant variation present in gene microarray expression datasets (or in any other similarly structured high-dimensional dataset). We applied these tools to two public datasets, and highlight sets of genes most affected by specific subsets of conditions (e.g. tissues, treatments, samples, etc.). Statistically significant associations for highlighted gene sets were shown via global analysis for Gene Ontology term enrichment. Together with covariate associations, the tool provides a basis for building testable hypotheses about the biological or experimental causes of observed variation.

Conclusion

We provide an unsupervised data mining technique for diverse microarray expression datasets that is distinct from major methods now in routine use. In test uses, this method, based on publicly available gene annotations, appears to identify numerous sets of biologically relevant genes. It has proven especially valuable in instances where there are many diverse conditions (10's to hundreds of different tissues or cell types), a situation in which many clustering and ordering algorithms become problematic. This approach also shows promise in other topic domains such as multi-spectral imaging datasets.
A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila
Authors: Pacifico Svetlana , Liu Guozhen , Guest Stephen , Parrish Jodi R , Fotouhi Farshad , Finley Russell L
Published: April 2006

Background

Biological processes are mediated by networks of interacting genes and proteins. Efforts to map and understand these networks are resulting in the proliferation of interaction data derived from both experimental and computational techniques for a number of organisms. The volume of this data combined with the variety of specific forms it can take has created a need for comprehensive databases that include all of the available data sets, and for exploration tools to facilitate data integration and analysis. One powerful paradigm for the navigation and analysis of interaction data is an interaction graph or map that represents proteins or genes as nodes linked by interactions. Several programs have been developed for graphical representation and analysis of interaction data, yet there remains a need for alternative programs that can provide casual users with rapid easy access to many existing and emerging data sets.

Description

Here we describe a comprehensive database of Drosophila gene and protein interactions collected from a variety of sources, including low and high throughput screens, genetic interactions, and computational predictions. We also present a program for exploring multiple interaction data sets and for combining data from different sources. The program, referred to as the Interaction Map (IM) Browser, is a web-based application for searching and visualizing interaction data stored in a relational database system. Use of the application requires no downloads and minimal user configuration or training, thereby enabling rapid initial access to interaction data. IM Browser was designed to readily accommodate and integrate new types of interaction data as it becomes available. Moreover, all information associated with interaction measurements or predictions and the genes or proteins involved are accessible to the user. This allows combined searches and analyses based on either common or technique-specific attributes. The data can be visualized as an editable graph and all or part of the data can be downloaded for further analysis with other tools for specific applications. The database is available at http://proteome.wayne.edu/PIMdb.html

Conclusion

The Drosophila Interactions Database described here places a variety of disparate data into one easily accessible location. The database has a simple structure that maintains all relevant information about how each interaction was determined. The IM Browser provides easy, complete access to this database and could readily be used to publish other sets of interaction data. By providing access to all of the available information from a variety of data types, the program will also facilitate advanced computational analyses.
A set of highly informative rat simple sequence length polymorphism (SSLP) markers and genetically defined rat strains
Authors: Mashimo Tomoji , Voigt Birger , Tsurumi Toshiko , Naoi Kuniko , Nakanishi Satoshi , Yamasaki Ken-ichi , Kuramoto Takashi , Serikawa Tadao
Published: April 2006

Background

The National Bio Resource Project for the Rat in Japan (NBRP-Rat) is focusing on collecting, preserving and distributing various rat strains, including spontaneous mutant, transgenic, congenic, and recombinant inbred (RI) strains. To evaluate their value as models of human diseases, we are characterizing them using 109 phenotypic parameters, such as clinical measurements, internal anatomy, metabolic parameters, and behavioral tests, as part of the Rat Phenome Project. Here, we report on a set of 357 simple sequence length polymorphism (SSLP) markers and 122 rat strains, which were genotyped by the marker set.

Results

The SSLP markers were selected according to their distribution patterns throughout the whole rat genome with an average spacing of 7.59 Mb. The average number of informative markers between all possible pairs of strains was 259 (72.5% of 357 markers), showing their high degree of polymorphism. From the genetic profile of these rat inbred strains, we constructed a rat family tree to clarify their genetic background.

Conclusion

These highly informative SSLP markers as well as genetically and phenotypically defined rat strains are useful for designing experiments for quantitative trait loci (QTL) analysis and to choose strategies for developing new genetic resources. The data and resources are freely available at the NBRP-Rat web site [1].
Multi-level gene expression profiles affected by thymidylate synthase and 5-fluorouracil in colon cancer
Authors: Xi Yaguang , Nakajima Go , Schmitz John C , Chu Edward , Ju Jingfang
Published: April 2006

Background

Thymidylate synthase (TS) is a critical target for cancer chemotherapy and is one of the most extensively studied biomarkers for fluoropyrimidine-based chemotherapy. In addition to its critical role in enzyme catalysis, TS functions as an RNA binding protein to regulate the expression of its own mRNA translation and other cellular mRNAs, such as p53, at the translational level. In this study, a comprehensive gene expression analysis at the levels of both transcriptional and post-transcriptional regulation was conducted to identify response markers using human genome array with TS-depleted human colon cancer HCT-C18 (TS-) cells and HCT-C18 (TS+) cells stably transfected with the human TS cDNA expression plasmid.

Results

A total of 38 genes were found to be significantly affected by TS based on the expression profiles of steady state mRNA transcripts. However, based on the expression profiles of polysome associated mRNA transcripts, over 149 genes were affected by TS overexpression. This indicates that additional post-transcriptionally controlled genes can be captured with profiling polysome associated mRNA population. This unique approach provides a comprehensive overview of genes affected by TS. Additional novel post-transcriptionally regulated genes affected by 5-fluorouracil (5-FU) treatment were also discovered via similar approach.

Conclusion

To our knowledge, this is the first time that a comprehensive gene expression profile regulated by TS and 5-FU was analyzed at the multiple steps of gene regulation. This study will provide candidate markers that can be potentially used for predicting therapeutic outcomes for fluoropyrimidine-based cancer chemotherapy.
Fast rate of evolution in alternatively spliced coding regions of mammalian genes
Authors: Ermakova Ekaterina O , Nurtdinov Ramil N , Gelfand Mikhail S
Published: April 2006

Background

At least half of mammalian genes are alternatively spliced. Alternative isoforms are often genome-specific and it has been suggested that alternative splicing is one of the major mechanisms for generating protein diversity in the course of evolution. Another way of looking at alternative splicing is to consider sequence evolution of constitutive and alternative regions of protein-coding genes. Indeed, it turns out that constitutive and alternative regions evolve in different ways.

Results

A set of 3029 orthologous pairs of human and mouse alternatively spliced genes was considered. The rate of nonsynonymous substitutions (dN), the rate of synonymous substitutions (dS), and their ratio (ω = dN/dS) appear to be significantly higher in alternatively spliced coding regions compared to constitutive regions. When N-terminal, internal and C-terminal alternatives are analysed separately, C-terminal alternatives appear to make the main contribution to the observed difference. The effects become even more pronounced in a subset of fast evolving genes.

Conclusion

These results provide evidence of weaker purifying selection and/or stronger positive selection in alternative regions and thus one more confirmation of accelerated evolution in alternative regions. This study corroborates the theory that alternative splicing serves as a testing ground for molecular evolution.
Alternative first exon splicing regulates subcellular distribution of methionine sulfoxide reductases
Authors: Kim Hwa-Young , Gladyshev Vadim N
Published: April 2006

Background

Methionine sulfoxide reduction is an important protein repair pathway that protects against oxidative stress, controls protein function and has a role in regulation of aging. There are two enzymes that reduce stereospecifically oxidized methionine residues: MsrA (methionine-S-sulfoxide reductase) and MsrB (methionine-R-sulfoxide reductase). In many organisms, these enzymes are targeted to various cellular compartments. In mammals, a single MsrA gene is known, however, its product is present in cytosol, nucleus, and mitochondria. In contrast, three mammalian MsrB genes have been identified whose products are located in different cellular compartments.

Results

In the present study, we identified and characterized alternatively spliced forms of mammalian MsrA. In addition to the previously known variant containing an N-terminal mitochondrial signal peptide and distributed between mitochondria and cytosol, a second mouse and human form was detected in silico. This form, MsrA(S), was generated using an alternative first exon. MsrA(S) was enzymatically active and was present in cytosol and nucleus in transfected cells, but occurred below detection limits in tested mouse tissues. The third alternative form lacked the active site and could not be functional. In addition, we found that mitochondrial and cytosolic forms of both MsrA and MsrB in Drosophila could be generated by alternative first exon splicing.

Conclusion

Our data suggest conservation of alternative splicing to regulate subcellular distribution of methionine sulfoxide reductases.
Upregulation of a tonoplast-localized cytochrome P450 during petal senescence in Petunia inflata
Authors: Xu Yan , Ishida Hiroyuki , Reisen Daniel , Hanson Maureen R
Published: April 2006

Background

Gene expression in Petunia inflata petals undergoes major changes following compatible pollination. Severe flower wilting occurs reproducibly within 36 hours, providing an excellent model for investigation of petal senescence and programmed cell death. Expression of a number of genes and various enzyme activities involved in the degradation and remobilization of macromolecules have been found to be upregulated during the early stages of petal senescence.

Results

By performing differential display of cDNAs during Petunia inflata petal senescence, a highly upregulated gene encoding a cytochrome P450 was identified. Analysis of the complete cDNA sequence revealed that the predicted protein is a member of the CYP74C family (CYP74C9) and is highly similar to a tomato CYP74C allene oxide synthase (AOS) that is known to be active on 9-hydroperoxides. Cloning of the petunia genomic DNA revealed an intronless gene with a promoter region that carries signals found in stress-responsive genes and potential binding sites for Myb transcription factors. Transcripts were present at detectable levels in root and stem, but were 40 times more abundant in flowers 36 hours after pollination. Ethylene and jasmonate treatment resulted in transitory increases in expression in detached flowers. A protein fusion of the CYP74C coding region to a C-terminal GFP was found to be located in the tonoplast.

Conclusion

Though oxylipins, particularly jasmonates, are known to be involved in stress responses, the role of other products of CYP74 enzymes is less well understood. The identification of a CYP74C family member as a highly upregulated gene during petal senescence suggests that additional products of fatty acid metabolism may play important roles during programmed cell death. In contrast to the chloroplast localization of AOS proteins in the CYP74A subfamily, GFP fusion data indicates that the petunia CYP74C9 enzyme is in the tonoplast. This result suggests that the highly similar CYP74C enzymes that have been identified in two other Solanaceous plants may also be associated with the vacuole, an organelle known to have a prominent role in programmed cell death.
High frequency oscillatory ventilation and prone positioning in a porcine model of lavage-induced acute lung injury
Authors: Brederlau Joerg , Muellenbach Ralf , Kredel Markus , Greim Clemens , Roewer Norbert
Published: April 2006

Background

This animal study was conducted to assess the combined effects of high frequency oscillatory ventilation (HFOV) and prone positioning on pulmonary gas exchange and hemodynamics.

Methods

Saline lung lavage was performed in 14 healthy pigs (54 ± 3.1 kg, mean ± SD) until the arterial oxygen partial pressure (PaO2) decreased to 55 ± 7 mmHg. The animals were ventilated in the pressure controlled mode (PCV) with a positive endexpiratory pressure (PEEP) of 5 cmH2O and a tidal volume (VT) of 6 ml/kg body weight. After a stabilisation period of 60 minutes, the animals were randomly assigned to 2 groups. Group 1: HFOV in supine position; group 2: HFOV in prone position. After evaluation of prone positioning in group 2, the mean airway pressure (Pmean) was increased by 3 cmH2O from 16 to 34 cmH2O every 20 minutes in both groups accompanied by measurements of respiratory and hemodynamic variables. Finally all animals were ventilated supine with PCV, PEEP = 5 cm H2O, VT = 6 ml/kg.

Results

Combination of HFOV with prone positioning improves oxygenation and results in normalisation of cardiac output and considerable reduction of pulmonary shunt fraction at a significant (p < 0.05) lower Pmean than HFOV and supine positioning.

Conclusion

If ventilator induced lung injury is ameliorated by a lower Pmean, a combined treatment approach using HFOV and prone positioning might result in further lung protection.
Estrogen-induced DNA synthesis in vascular endothelial cells is mediated by ROS signaling
Authors: Felty Quentin
Published: April 2006

Background

Since estrogen is known to increase vascular endothelial cell growth, elevated estrogen exposure from hormone replacement therapy or oral contraceptives has the potential to contribute in the development of abnormal proliferative vascular lesions and subsequent thickening of the vasculature. How estrogen may support or promote vascular lesions is not clear. We have examined in this study whether estrogen exposure to vascular endothelial cells increase the formation of reactive oxygen species (ROS), and estrogen-induced ROS is involved in the growth of endothelial cells.

Methods

The effect of estrogen on the production of intracellular oxidants and the role of estrogen-induced ROS on cell growth was studied in human umbilical vein endothelial cells. ROS were measured by monitoring the oxidation of 2'7'-dichlorofluorescin by spectrofluorometry. Endothelial cell growth was measured by a colorimetric immunoassay based on BrdU incorporation into DNA.

Results

Physiological concentrations of estrogen (367 fmol and 3.67 pmol) triggered a rapid 2-fold increase in intracellular oxidants in endothelial cells. E2-induced ROS formation was inhibited to basal levels by cotreatment with the mitochondrial inhibitor rotenone (2 μM) and xanthine oxidase inhibitor allopurinol (50 μM). Inhibitors of NAD(P)H oxidase, apocynin and DPI, did not block E2-induced ROS formation. Furthermore, the NOS inhibitor, L-NAME, did not prevent the increase in E2-induced ROS. These findings indicate both mitochondria and xanthine oxidase are the source of ROS in estrogen treated vascular endothelial cells. E2 treated cells showed a 2-fold induction of BrdU incorporation at 18 h which was not observed in cells exposed to vehicle alone. Cotreatment with ebselen (20 μM) and NAC (1 mM) inhibited E2-induced BrdU incorporation without affecting the basal levels of DNA synthesis. The observed inhibitory effect of NAC and ebselen on E2-induced DNA synthesis was also shown to be dose dependent.

Conclusion

We have shown that estrogen exposure stimulates the rapid production of intracellular ROS and they are involved in growth signaling of endothelial cells. It appears that the early estrogen signaling does not require estrogen receptor genomic signaling because we can inhibit estrogen-induced DNA synthesis by antioxidants. Findings of this study may further expand research defining the underlying mechanism of how estrogen may promote vascular lesions. It also provides important information for the design of new antioxidant-based drugs or new antioxidant gene therapy to protect the cardiovascular health of individuals sensitive to estrogen.