bluuebunny/crossref_metadata_2025 huggingface dataset:
Posttraumatic Shame and Guilt
Authors: Wilson John P. , Droždek Boris , Turkovic Silvana
Published: March 2006

Posttraumatic shame and guilt are important dimensions of posttraumatic syndromes, including simple and complex post-traumatic stress disorder (PTSD). The concepts of posttraumatic shame and guilt have received little theoretical or empirical investigation in the field of traumatology. It is proposed that there are acute and prolonged states of posttraumatic shame and guilt that can be compared in their consequences across eight psychosocial dimensions: (a) self-attribution processes, (b) emotional states and capacity for affect regulation, (c) appraisal and interpretation of actions, (d) the impact of states of shame and guilt on personal identity, (e) suicidality, (f) defensive patterns, (g) proneness to psychopathology and PTSD, and (h) the dimensions of the self-structure adversely affected by states of posttraumatic shame and guilt. The experience of posttraumatic states of shame and guilt are associated with compounded affective processesin PTSD, depression, and substance use disorders.
Family Violence in the Military
Authors: Rentz E. Danielle , Martin Sandra L. , Gibbs Deborah A. , Clinton-Sherrod Monique , Hardison Jennifer , Marshall Stephen W.
Published: March 2006

Family violence, including both child maltreatment and spouse abuse, is a public health concern in both military and civilian populations. However, there is limited knowledge concerning violence in military families relative to civilian families. This literature review critically reviews studies that examine child maltreatment and spouse abuse among military families and compares family violence in military versus nonmilitary populations. Physical abuse and neglect compose the majority of the reported and substantiated cases of child maltreatment in military families, followed by sexual abuse and emotional abuse. On the other hand, physical abuse represents more than 90% of all substantiated cases of spouse abuse in military families, followed by emotional abuse, neglect, and sexual abuse. Mixed results were found when comparing military and nonmilitary families in terms of child maltreatment and spouse abuse, in part because of a lack of consistency in policies and practices between military and civilian agencies.
Can We Prevent Road Rage?
Authors: Asbridge Mark , Smart Reginald G. , Mann Robert E.
Published: March 2006

Road rage has become a serious concern in many countries, and preventive efforts are required. This article reviews what can be done to prevent road rage by exploring potential prevention avenues in five areas. First, legal changes aimed at increasing the penalties for road rage behavior could be instituted, drawing on models from aggressive-driving or impaired-driving laws. A second approach would involve the adoption of court programs for convicted road ragers. Third, car redesign offers a means of reducing crime through environmental design. Fourth, mass media education could be implemented to inform drivers of the risk from road rage and how to avoid situations that facilitate road rage. Finally, prevention efforts could be directed to long-term societal changes that emphasize structural modifications, such as reducing congestion on the roads, reduced driver stress, or promoting public transportation. The strengths and weaknesses of these strategies are discussed.
Deconstructing Diversity Discourses in the Field of Educational Management and Leadership
Authors: Blackmore Jill
Published: March 2006

Discourses of diversity have supplanted those of equal opportunity or social justice in many Western democratic societies. While the notion of diversity is seemingly empowering through its recognition of cultural, religious, racial and gender difference within nation states, the emergence of this discourse during the 1990s has been in the context of neoliberal managerialist discourses that assume social action is fully explicable through theories of maximizing self interest. Thus notions of diversity, while originating in collective demands of social movements of feminism, anti racism and multiculturalism of the 1970s and 1980s, have in recent times privileged learning and leadership as an individual accomplishment and not a collective practice. Thus the dominant discourse of diversity is more in alignment with the deregulatory aspects of the increasingly managerial and market orientation of schooling, decentring earlier discourses of more transformatory notions premised upon reducing inequality and discrimination and developing ‘inclusivity’ in and through schooling. This paper provides a contextual and conceptual framework through which to explore the intersections and divergences of discourses of diversity in schools and their practical application.
Walking between Two Worlds
Authors: Fitzgerald Tanya
Published: March 2006

Theory and research in the field of educational leadership and management has grown exponentially in the past decade. I am troubled however by the apparent primacy of ethnocentric ways of knowing, acting and leading. And while we might heed Dimmock and Walker’s call for a cross-cultural approach to leadership and management, located at the periphery are bodies of knowledge for/about Indigenous ways of leading and being led. This article reports on a three-year research project conducted in New Zealand, Australia and Canada for/with Indigenous women. Evidence points to the triple bind Indigenous women face due to exigencies of race and gender and the two worlds they occupy; the Indigenous and the non-Indigenous.
Leading Multiethnic Schools
Authors: Shah Saeeda
Published: March 2006

In the context of emigration, immigration, international mobility and globalization, the management contexts of education sites are undergoing deep and sensitive changes making challenging demands on educational leaders. Multiethnic/multicultural schools are emerging as a long-term phenomenon in countries such as Britain against the backdrop of international socio-eco-political developments. The article focuses on the issue of ethnic identity, exploring its effect on leadership effectiveness and student achievement, with a focus on British secondary schools. The issues discussed include the construction and projection of identities, the interplay between the discourses of identity and the students’ achievement, leadership and management as it relates to student identities and the management of conflict and tensions in multiethnic schools. The final section suggests a way forward by offering some insights into developing school leadership to engage with wider diversity in complex contexts such as multiethnic Britain and to improve understanding of leading multiethnic schools.
Who Gets Ahead?
Authors: Wilson Valerie , Powney Janet , Hall Stuart , Davidson Julia
Published: March 2006

This article reports the results from a 12-month study of teachers’ career progress in schools in England and the ways in which headteachers and teachers perceive that age, disability, ethnicity and gender affect teachers’ career prospects. Many teachers thought that they had been promoted because of their personal traits, such as drive, confidence and ability, and there was little evidence of direct discrimination. However, certain groups of teachers, for example part-time and supply staff, mature entrants to teaching, members of minority ethnic groups, teachers with disabilities, older male and female teachers, female teachers with children, all believed that their personal characteristics had disadvantaged their career progression. The study offers some insight into the structural constraints that hinder teachers’ careers and how greater diversity among promoted staff in schools might be achieved. The implications for school leaders are highlighted.
BCR/ABL kinase induces self-mutagenesis via reactive oxygen species to encode imatinib resistance
Authors: Koptyra Mateusz , Falinski Rafal , Nowicki Michal O. , Stoklosa Tomasz , Majsterek Ireneusz , Nieborowska-Skorska Margaret , Blasiak Janusz , Skorski Tomasz
Published: March 2006

Mutations in the BCR/ABL kinase domain play a major role in resistance to imatinib mesylate (IM). We report here that BCR/ABL kinase stimulates reactive oxygen species (ROS), which causes oxidative DNA damage, resulting in mutations in the kinase domain. The majority of mutations involved A/T→G/C and G/C→A/T transitions, a phenotype detected previously in patients, which encoded clinically relevant amino acid substitutions, causing IM resistance. This effect was reduced in cells expressing BCR/ABL(Y177F) mutant, which does not elevate ROS. Inhibition of ROS in leukemia cells by the antioxidants pyrrolidine dithiocarbamate (PDTC), N-acetylcysteine (NAC), and vitamin E (VE) decreased the mutagenesis rate and frequency of IM resistance. Simultaneous administration of IM and an antioxidant exerted better antimutagenic effect than an antioxidant alone. Therefore, inhibition of ROS should diminish mutagenesis and enhance the effectiveness of IM. (Blood. 2006;108:319-327)
Peroxisome proliferator-activated receptor γ (PPARγ) ligands reverse CTL suppression by alternatively activated (M2) macrophages in cancer
Authors: Van Ginderachter Jo A. , Meerschaut Sofie , Liu Yuanqing , Brys Lea , De Groeve Kurt , Hassanzadeh Ghassabeh Gholamreza , Raes Geert , De Baetselier Patrick
Published: March 2006

Tumors may escape from immune control by the induction of CD11b+Gr-1+ myeloid suppressor cells in the spleen. In this study, we demonstrate that this cell population can be subdivided into a CD11bhiGr-1intSSCloLy6GnegM-CSFRint immature monocytic fraction and a CD11bhi+Gr-1hiSSChiLy6GhiM-CSFRneg granulocytic fraction. Upon in vitro culture, the monocytic CD11b+Gr-1+ cell fraction is sufficient for cytotoxic T lymphocyte (CTL) suppression, which is linked to the gradual differentiation of these monocytic cells into mature F4/80+ CD68+ macrophages. These CTL-suppressive macrophages are alternatively activated (M2), as demonstrated by the expression of known and novel M2 signature genes. In search of M2-associated genes involved in the suppressive activity, it is shown that stimulation of peroxisome proliferator-activated receptor γ (PPARγ) and inhibition of phospholipase A2 (PLA2) activity cooperate to alleviate CTL suppression. Of importance, purified tumor-associated macrophages display a similar M2 phenotype and are suppressive for antitumor CTLs, via a mechanism that can be almost completely reversed by PPARγ ligands. Overall, our data identify PLA2 and especially PPARγ as new potential therapeutic targets to subvert macrophage-mediated CTL suppression in cancer.
Maintained inspiratory activity during proportional assist ventilation in surfactant-depleted cats early after surfactant instillation: phrenic nerve and pulmonary stretch receptor activity
Authors: Sindelar Richard , Rieger-Fackeldey Esther , Jonzon Anders , Schaller Peter , Schulze Andreas , Sedin Gunnar
Published: March 2006

Background

Inspiratory activity is a prerequisite for successful application of patient triggered ventilation such as proportional assist ventilation (PAV). It has recently been reported that surfactant instillation increases the activity of slowly adapting pulmonary stretch receptors (PSRs) followed by a shorter inspiratory time (Sindelar et al, J Appl Physiol, 2005 [Epub ahead of print]). Changes in lung mechanics, as observed in preterm infants with respiratory distress syndrome and after surfactant treatment, might therefore influence the inspiratory activity when applying PAV early after surfactant treatment.

Objective

To investigate the regulation of breathing and ventilatory response in surfactant-depleted young cats during PAV and during continuous positive airway pressure (CPAP) early after surfactant instillation in relation to phrenic nerve activity (PNA) and the activity of PSRs.

Methods

Seven anesthetized, endotracheally intubated young cats were exposed to periods of CPAP and PAV with the same end-expiratory pressure (0.2–0.5 kPa) before and after lung lavage and after surfactant instillation. PAV was set to compensate for 75% of the lung elastic recoil.

Results

Tidal volume and respiratory rate were higher with lower PaCO2 and higher PaO2 during PAV than during CPAP both before and after surfactant instillation (p < 0.05; both conditions). As an indicator of breathing effort, esophageal deflection pressure and PNA were lower during PAV than during CPAP in both conditions (p < 0.02). Peak PSR activity was higher and occurred earlier during PAV than during CPAP (p < 0.01), and correlated linearly with PNA duration in all conditions studied (p < 0.001). The inspiratory time decreased as tidal volume increased when CPAP was changed to PAV, with the highest correlation observed after surfactant instillation (r = -0.769). No apneic periods could be observed.

Conclusion

PSR activity and the control of breathing are maintained during PAV in surfactant-depleted cats early after surfactant instillation, with a higher ventilatory response and a lower breathing effort than during CPAP.
SimArray: a user-friendly and user-configurable microarray design tool
Authors: Auburn Richard P , Russell Roslin R , Fischer Bettina , Meadows Lisa A , Sevillano Matilla Santiago , Russell Steven
Published: March 2006

Background

Microarrays were first developed to assess gene expression but are now also used to map protein-binding sites and to assess allelic variation between individuals. Regardless of the intended application, efficient production and appropriate array design are key determinants of experimental success. Inefficient production can make larger-scale studies prohibitively expensive, whereas poor array design makes normalisation and data analysis problematic.

Results

We have developed a user-friendly tool, SimArray, which generates a randomised spot layout, computes a maximum meta-grid area, and estimates the print time, in response to user-specified design decisions. Selected parameters include: the number of probes to be printed; the microtitre plate format; the printing pin configuration, and the achievable spot density. SimArray is compatible with all current robotic spotters that employ 96-, 384- or 1536-well microtitre plates, and can be configured to reflect most production environments. Print time and maximum meta-grid area estimates facilitate evaluation of each array design for its suitability. Randomisation of the spot layout facilitates correction of systematic biases by normalisation.

Conclusion

SimArray is intended to help both established researchers and those new to the microarray field to develop microarray designs with randomised spot layouts that are compatible with their specific production environment. SimArray is an open-source program and is available from http://www.flychip.org.uk/SimArray/.
The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies
Authors: Verhaak Roel GW , Staal Frank JT , Valk Peter JM , Lowenberg Bob , Reinders Marcel JT , de Ridder Dick
Published: March 2006

Background

Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set expression values. Various pre-processing techniques, such as dChip, GCRMA, RMA and MAS have been developed for this purpose. This study assesses the effect of applying different pre-processing methods on the results of analyses of large Affymetrix datasets. By focusing on practical applications of microarray-based research, this study provides insight into the relevance of pre-processing procedures to biology-oriented researchers.

Results

Using two publicly available datasets, i.e., gene-expression data of 285 patients with Acute Myeloid Leukemia (AML, Affymetrix HG-U133A GeneChip) and 42 samples of tumor tissue of the embryonal central nervous system (CNS, Affymetrix HuGeneFL GeneChip), we tested the effect of the four pre-processing strategies mentioned above, on (1) expression level measurements, (2) detection of differential expression, (3) cluster analysis and (4) classification of samples. In most cases, the effect of pre-processing is relatively small compared to other choices made in an analysis for the AML dataset, but has a more profound effect on the outcome of the CNS dataset. Analyses on individual probe sets, such as testing for differential expression, are affected most; supervised, multivariate analyses such as classification are far less sensitive to pre-processing.

Conclusion

Using two experimental datasets, we show that the choice of pre-processing method is of relatively minor influence on the final analysis outcome of large microarray studies whereas it can have important effects on the results of a smaller study. The data source (platform, tissue homogeneity, RNA quality) is potentially of bigger importance than the choice of pre-processing method.
Evaluation of absolute quantitation by nonlinear regression in probe-based real-time PCR
Authors: Goll Rasmus , Olsen Trine , Cui Guanglin , Florholmen Jon
Published: March 2006

Background

In real-time PCR data analysis, the cycle threshold (CT) method is currently the gold standard. This method is based on an assumption of equal PCR efficiency in all reactions, and precision may suffer if this condition is not met. Nonlinear regression analysis (NLR) or curve fitting has therefore been suggested as an alternative to the cycle threshold method for absolute quantitation. The advantages of NLR are that the individual sample efficiency is simulated by the model and that absolute quantitation is possible without a standard curve, releasing reaction wells for unknown samples. However, the calculation method has not been evaluated systematically and has not previously been applied to a TaqMan platform. Aim: To develop and evaluate an automated NLR algorithm capable of generating batch production regression analysis.

Results

Total RNA samples extracted from human gastric mucosa were reverse transcribed and analysed for TNFA, IL18 and ACTB by TaqMan real-time PCR. Fluorescence data were analysed by the regular CT method with a standard curve, and by NLR with a positive control for conversion of fluorescence intensity to copy number, and for this purpose an automated algorithm was written in SPSS syntax. Eleven separate regression models were tested, and the output data was subjected to Altman-Bland analysis. The Altman-Bland analysis showed that the best regression model yielded quantitative data with an intra-assay variation of 58% vs. 24% for the CT derived copy numbers, and with a mean inter-method deviation of × 0.8.

Conclusion

NLR can be automated for batch production analysis, but the CT method is more precise for absolute quantitation in the present setting. The observed inter-method deviation is an indication that assessment of the fluorescence conversion factor used in the regression method can be improved. However, the versatility depends on the level of precision required, and in some settings the increased cost effectiveness of NLR may justify the lower precision.
Metabolite coupling in genome-scale metabolic networks
Authors: Becker Scott A , Price Nathan D , Palsson Bernhard Ø
Published: March 2006

Background

Biochemically detailed stoichiometric matrices have now been reconstructed for various bacteria, yeast, and for the human cardiac mitochondrion based on genomic and proteomic data. These networks have been manually curated based on legacy data and elementally and charge balanced. Comparative analysis of these well curated networks is now possible. Pairs of metabolites often appear together in several network reactions, linking them topologically. This co-occurrence of pairs of metabolites in metabolic reactions is termed herein "metabolite coupling." These metabolite pairs can be directly computed from the stoichiometric matrix, S. Metabolite coupling is derived from the matrix ŜŜ
T, whose off-diagonal elements indicate the number of reactions in which any two metabolites participate together, where Ŝ is the binary form of S.

Results

Metabolite coupling in the studied networks was found to be dominated by a relatively small group of highly interacting pairs of metabolites. As would be expected, metabolites with high individual metabolite connectivity also tended to be those with the highest metabolite coupling, as the most connected metabolites couple more often. For metabolite pairs that are not highly coupled, we show that the number of reactions a pair of metabolites shares across a metabolic network closely approximates a line on a log-log scale. We also show that the preferential coupling of two metabolites with each other is spread across the spectrum of metabolites and is not unique to the most connected metabolites. We provide a measure for determining which metabolite pairs couple more often than would be expected based on their individual connectivity in the network and show that these metabolites often derive their principal biological functions from existing in pairs. Thus, analysis of metabolite coupling provides information beyond that which is found from studying the individual connectivity of individual metabolites.

Conclusion

The coupling of metabolites is an important topological property of metabolic networks. By computing coupling quantitatively for the first time in genome-scale metabolic networks, we provide insight into the basic structure of these networks.
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
Authors: MacIsaac Kenzie D , Wang Ting , Gordon D Benjamin , Gifford David K , Stormo Gary D , Fraenkel Ernest
Published: March 2006

Background

The regulatory map of a genome consists of the binding sites for proteins that determine the transcription of nearby genes. An initial regulatory map for S. cerevisiae was recently published using six motif discovery programs to analyze genome-wide chromatin immunoprecipitation data for 203 transcription factors. The programs were used to identify sequence motifs that were likely to correspond to the DNA-binding specificity of the immunoprecipitated proteins. We report improved versions of two conservation-based motif discovery algorithms, PhyloCon and Converge. Using these programs, we create a refined regulatory map for S. cerevisiae by reanalyzing the same chromatin immunoprecipitation data.

Results

Applying the same conservative criteria that were applied in the original study, we find that PhyloCon and Converge each separately discover more known specificities than the combination of all six programs in the previous study. Combining the results of PhyloCon and Converge, we discover significant sequence motifs for 36 transcription factors that were previously missed. The new set of motifs identifies 636 more regulatory interactions than the previous one. The new network contains 28% more regulatory interactions among transcription factors, evidence of greater cross-talk between regulators.

Conclusion

Combining two complementary computational strategies for conservation-based motif discovery improves the ability to identify the specificity of transcriptional regulators from genome-wide chromatin immunoprecipitation data. The increased sensitivity of these methods significantly expands the map of yeast regulatory sites without the need to alter any of the thresholds for statistical significance. The new map of regulatory sites reveals a more elaborate and complex view of the yeast genetic regulatory network than was observed previously.
Machine learning approaches to supporting the identification of photoreceptor-enriched genes based on expression data
Authors: Wang Haiying , Zheng Huiru , Simpson David , Azuaje Francisco
Published: March 2006

Background

Retinal photoreceptors are highly specialised cells, which detect light and are central to mammalian vision. Many retinal diseases occur as a result of inherited dysfunction of the rod and cone photoreceptor cells. Development and maintenance of photoreceptors requires appropriate regulation of the many genes specifically or highly expressed in these cells. Over the last decades, different experimental approaches have been developed to identify photoreceptor enriched genes. Recent progress in RNA analysis technology has generated large amounts of gene expression data relevant to retinal development. This paper assesses a machine learning methodology for supporting the identification of photoreceptor enriched genes based on expression data.

Results

Based on the analysis of publicly-available gene expression data from the developing mouse retina generated by serial analysis of gene expression (SAGE), this paper presents a predictive methodology comprising several in silico models for detecting key complex features and relationships encoded in the data, which may be useful to distinguish genes in terms of their functional roles. In order to understand temporal patterns of photoreceptor gene expression during retinal development, a two-way cluster analysis was firstly performed. By clustering SAGE libraries, a hierarchical tree reflecting relationships between developmental stages was obtained. By clustering SAGE tags, a more comprehensive expression profile for photoreceptor cells was revealed. To demonstrate the usefulness of machine learning-based models in predicting functional associations from the SAGE data, three supervised classification models were compared. The results indicated that a relatively simple instance-based model (KStar model) performed significantly better than relatively more complex algorithms, e.g. neural networks. To deal with the problem of functional class imbalance occurring in the dataset, two data re-sampling techniques were studied. A random over-sampling method supported the implementation of the most powerful prediction models. The KStar model was also able to achieve higher predictive sensitivities and specificities using random over-sampling techniques.

Conclusion

The approaches assessed in this paper represent an efficient and relatively inexpensive in silico methodology for supporting large-scale analysis of photoreceptor gene expression by SAGE. They may be applied as complementary methodologies to support functional predictions before implementing more comprehensive, experimental prediction and validation methods. They may also be combined with other large-scale, data-driven methods to facilitate the inference of transcriptional regulatory networks in the developing retina. Furthermore, the methodology assessed may be applied to other data domains.
Microbial identification by mass cataloging
Authors: Zhang Zhengdong , Jackson George W , Fox George E , Willson Richard C
Published: March 2006

Background

The public availability of over 180,000 bacterial 16S ribosomal RNA (rRNA) sequences has facilitated microbial identification and classification using hybridization and other molecular approaches. In their usual format, such assays are based on the presence of unique subsequences in the target RNA and require a prior knowledge of what organisms are likely to be in a sample. They are thus limited in generality when analyzing an unknown sample.

Herein, we demonstrate the utility of catalogs of masses to characterize the bacterial 16S rRNA(s) in any sample. Sample nucleic acids are digested with a nuclease of known specificity and the products characterized using mass spectrometry. The resulting catalogs of masses can subsequently be compared to the masses known to occur in previously-sequenced 16S rRNAs allowing organism identification. Alternatively, if the organism is not in the existing database, it will still be possible to determine its genetic affinity relative to the known organisms.

Results

Ribonuclease T1 and ribonuclease A digestion patterns were calculated for 1,921 complete 16S rRNAs. Oligoribonucleotides generated by RNase T1 of length 9 and longer produce sufficient diversity of masses to be informative. In addition, individual fragments or combinations thereof can be used to recognize the presence of specific organisms in a complex sample. In this regard, 140 strains out of 1,921 organisms (7.3%) could be identified by the presence of a unique RNase T1-generated oligoribonucleotide mass. Combinations of just two and three oligoribonucleotide masses allowed 54% and 72% of the specific strains to be identified, respectively. An initial algorithm for recovering likely organisms present in complex samples is also described.

Conclusion

The use of catalogs of compositions (masses) of characteristic oligoribonucleotides for microbial identification appears extremely promising. RNase T1 is more useful than ribonuclease A in generating characteristic masses, though RNase A produces oligomers which are more readily distinguished due to the large mass difference between A and G. Identification of multiple species in mixtures is also feasible. Practical applicability of the method depends on high performance mass spectrometric determination, and/or use of methods that increase the one dalton (Da) mass difference between uracil and cytosine.
Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information
Authors: Song Jiangning , Burrage Kevin , Yuan Zheng , Huber Thomas
Published: March 2006

Background

The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function.

Results

In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively.

Conclusion

A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.
REtools: A laboratory program for restriction enzyme work: enzyme selection and reaction condition assistance
Authors: Martin Patrick , Boulukos Kim E , Pognonec Philippe
Published: March 2006

Background

Restriction enzymes are one of the everyday tools used in molecular biology. The continuously expanding panel of known restriction enzymes (several thousands) renders their optimal use virtually impossible without computerized assistance. Several manufacturers propose on-line sites that assist scientists in their restriction enzyme work, however, none of these sites meet all the actual needs of laboratory workers, and they do not take into account the enzymes actually present in one's own laboratory.

Results

Using FileMaker Pro, we developed a stand-alone application which can run on both PCs and Macintoshes. We called it REtools, for Restriction Enzyme tools. This program, which references all currently known enzymes (>3500), permits the creation and update of a personalized list of restriction enzymes actually available in one's own laboratory. Upon opening the program, scientists will be presented with a user friendly interface that will direct them to different menus, each one corresponding to different situations that restriction enzyme users commonly encounter. We particularly emphasized the ease of use to make REtools a solution that laboratory members would actually want to use.

Conclusion

REtools, a user friendly and easily customized program to organize any laboratory enzyme stock, brings a software solution that will make restriction enzyme use and reaction condition determination straightforward and efficient. The usually unexplored potential of isoschizomers also becomes accessible to all, since REtools proposes all possible enzymes similar to the one(s) chosen by the user. Finally, many of the commonly overlooked subtleties of restriction enzyme work, such as methylation requirement, unusual reaction conditions, or the number of flanking bases required for cleavage, are automatically provided by REtools.
Disruption of nucleocytoplasmic trafficking of cyclin D1 and topoisomerase II by sanguinarine
Authors: Holy Jon , Lamont Genelle , Perkins Edward
Published: March 2006

Background

The quaternary isoquinoline alkaloid sanguinarine is receiving increasing attention as a potential chemotherapeutic agent in the treatment of cancer. Previous studies have shown that this DNA-binding phytochemical can arrest a number of different types of transformed cells in G0/G1, and upregulate the CKIs p21 and p27 while downregulating multiple cyclins and CDKs. To more closely examine the responses of some of these cell cycle regulatory molecules to sanguinarine, we used immunocytochemical methods to visualize cyclin D1 and topoisomerase II behavior in MCF-7 breast cancer cells.

Results

5 – 10 μM sanguinarine effectively inhibits MCF-7 proliferation after a single application of drug. This growth inhibition is accompanied by a striking relocalization of cyclin D1 and topoisomerase II from the nucleus to the cytoplasm, and this effect persists for at least three days after drug addition. DNA synthesis is transiently inhibited by sanguinarine, but cells recover their ability to synthesize DNA within 24 hours. Taking advantage of the fluorescence characteristics of sanguinarine to follow its uptake and distribution suggests that these effects arise from a window of activity of a few hours immediately after drug addition, when sanguinarine is concentrated in the nucleus. These effects occur in morphologically healthy-looking cells, and thus do not simply represent part of an apoptotic response.

Conclusion

It appears that sub-apoptotic concentrations of sanguinarine can suppress breast cancer cell proliferation for extended lengths of time, and that this effect results from a relatively brief period of activity when the drug is concentrated in the nucleus. Sanguinarine transiently inhibits DNA synthesis, but a novel mechanism of action appears to involve disrupting the trafficking of a number of molecules involved in cell cycle regulation and progression. The ability of sub-apoptotic concentrations of sanguinarine to inhibit cell growth may be a useful feature for potential chemotherapeutic applications; however, a narrow effective range for these effects may exist.
Aging of mesenchymal stem cell in vitro
Authors: Bonab Mandana Mohyeddin , Alimoghaddam Kamran , Talebian Fatemeh , Ghaffari Syed Hamid , Ghavamzadeh Ardeshir , Nikbin Behrouz
Published: March 2006

Background

A hot new topic in medical treatment is the use of mesenchymal stem cells (MSC) in therapy. The low frequency of this subpopulation of stem cells in bone marrow (BM) necessitates their in vitro expansion prior to clinical use. We evaluated the effect of long term culture on the senescence of these cells.

Results

The mean long term culture was 118 days and the mean passage number was 9. The average number of PD decreased from 7.7 to 1.2 in the 10th passage. The mean telomere length decreased from 9.19 Kbp to 8.7 kbp in the 9th passage. Differentiation potential dropped from the 6th passage on. The culture's morphological abnormalities were typical of the Hayflick model of cellular aging.

Conclusion

We believe that MSC enter senescence almost undetectably from the moment of in vitro culturing. Simultaneously these cells are losing their stem cell characteristics. Therefore, it is much better to consider them for cell and gene therapy early on.
The evolution of the histone methyltransferase gene Su(var)3-9 in metazoans includes a fusion with and a re-fission from a functionally unrelated gene
Authors: Krauss Veiko , Fassl Anne , Fiebig Petra , Patties Ina , Sass Heinz
Published: March 2006

Background

In eukaryotes, histone H3 lysine 9 (H3K9) methylation is a common mechanism involved in gene silencing and the establishment of heterochromatin. The loci of the major heterochromatic H3K9 methyltransferase Su(var)3-9 and the functionally unrelated γ subunit of the translation initiation factor eIF2 are fused in Drosophila melanogaster. Here we examined the phylogenetic distribution of this unusual gene fusion and the molecular evolution of the H3K9 HMTase Su(var)3-9.

Results

We show that the gene fusion had taken place in the ancestral line of winged insects and silverfishs (Dicondylia) about 400 million years ago. We cloned Su(var)3-9 genes from a collembolan and a spider where both genes ancestrally exist as independent transcription units. In contrast, we found a Su(var)3-9-specific exon inside the conserved intron position 81-1 of the eIF2γ gene structure in species of eight different insect orders. Intriguinly, in the pea aphid Acyrthosiphon pisum, we detected only sequence remains of this Su(var)3-9 exon in the eIF2γ intron, along with an eIF2γ-independent Su(var)3-9 gene. This reveals an evolutionary re-fission of both genes in aphids. Su(var)3-9 chromo domains are similar to HP1 chromo domains, which points to a potential binding activity to methylated K9 of histone H3. SET domain comparisons suggest a weaker methyltransferase activity of Su(var)3-9 in comparison to other H3K9 HMTases. Astonishingly, 11 of 19 previously described, deleterious amino acid substitutions found in Drosophila Su(var)3-9 are seemingly compensable through accompanying substitutions during evolution.

Conclusion

Examination of the Su(var)3-9 evolution revealed strong evidence for the establishment of the Su(var)3-9/eIF2γ gene fusion in an ancestor of dicondylic insects and a re-fission of this fusion during the evolution of aphids. Our comparison of 65 selected chromo domains and 93 selected SET domains from Su(var)3-9 and related proteins offers functional predictions concerning both domains in Su(var)3-9 proteins.
Immune function and parasite resistance in male and polymorphic female Coenagrion puella
Authors: Joop Gerrit , Mitschke Andreas , Rolff Jens , Siva-Jothy Michael T
Published: March 2006

Background

Colour polymorphisms are widespread and one of the prime examples is the colour polymorphism in female coenagrionid damselflies: one female morph resembles the male colour (andromorph) while one, or more, female morphs are described as typically female (gynomorph). However, the selective pressures leading to the evolution and maintenance of this polymorphism are not clear. Here, based on the hypothesis that coloration and especially black patterning can be related to resistance against pathogens, we investigated the differences in immune function and parasite resistance between the different female morphs and males.

Results

Our studies of immune function revealed no differences in immune function between the female morphs but between the sexes in adult damselflies. In an experimental infection females infected shortly after emergence showed a higher resistance against a fungal pathogen than males, however female morphs did not differ in resistance. In a field sample of adult damselflies we did not find differences in infection rates with watermites and gregarines.

Conclusion

With respect to resistance and immune function 'andromorph' blue females of Coenagrion puella do not resemble the males. Therefore the colour polymorphism in coenagrionid damselflies is unlikely to be maintained by differences in immunity.
Search for genetic variants in the p66Shc longevity gene by PCR-single strand conformational polymorphism in patients with early-onset cardiovascular disease
Authors: Sentinelli Federica , Romeo Stefano , Barbetti Fabrizio , Berni Andrea , Filippi Emanuela , Fanelli Marzia , Fallarino Mara , Baroni Marco G
Published: March 2006

Background

Among the possible candidate genes for atherosclerosis experimental data point towards the longevity gene p66Shc. The p66Shc gene determines an increase of intracellular reactive oxygen species (ROS), affecting the rate of oxidative damage to nucleic acids. Knock-out p66Shc-/- mice show reduction of systemic oxidative stress, as well as of plasma LDL oxidation, and reduced atherogenic lesions. Thus, p66Shc may play a pivotal role in controlling oxidative stress and vascular dysfunction in vivo.

Methods

We searched for sequence variations in the p66Shc specific region of the Shc gene and its upstream promoter by PCR-SSCP in a selected group of early onset coronary artery disease (CAD) subjects (n. 78, mean age 48.5 ± 6 years) and in 93 long-living control subjects (mean age 89 ± 6 years).

Results

The analysis revealed two variant bands. Sequencing of these variants showed two SNPs: -354T>C in the regulatory region of p66Shc locus and 92C>T in the p66 specific region (CH2). Both these variants have never been described before. The first substitution partially modifies the binding consensus sequence of the Sp1 transcription factor, and was detected only in two heterozygous carriers (1 CAD subjects and 1 control subject). The 92C>T substitution in the CH2 region consists in an amino acid substitution at codon 31 (proline to leucine, P31L), and was detected in heterozygous status only in one CAD subject. No subjects homozygous for the two newly described SNPs were found.

Conclusion

Only two sequence variations in the p66Shc gene were observed in a total of 171 subjects, and only in heterozygotes. Our observations, in accordance to other studies, suggest that important variations in the p66Shc gene may be extremely rare and probably this gene is not involved in the genetic susceptibility to CAD.
QTL for microstructural and biophysical muscle properties and body composition in pigs
Authors: Wimmers Klaus , Fiedler Ilse , Hardge Torsten , Murani Eduard , Schellander Karl , Ponsuksili Siriluck
Published: March 2006

Background

The proportion of muscle fibre types and their size affect muscularity as well as functional properties of the musculature and meat quality. We aimed to identify QTL for microstructural muscle properties including muscle fibre size, their numbers and fibre type proportions as well as biophysical parameters of meat quality and traits related to body composition, i.e. pH, conductivity, area of M. longissimus dorsi and lean meat content. A QTL scan was conducted in a porcine experimental population that is based on Duroc and Berlin Miniature Pig.

Results

Least square regression interval mapping revealed five significant and 42 suggestive QTL for traits related to muscle fibre composition under the line-cross model as well as eight significant and 40 suggestive QTL under the half-sib model. For traits related to body composition and biophysical parameters of meat quality five and twelve significant plus nine and 22 suggestive QTL were found under the line-cross and half-sib model, respectively. Regions with either significant QTL for muscle fibre traits or significant QTL for meat quality and muscularity or both were detected on SSC1, 2, 3, 4, 5, 13, 14, 15, and 16. QTL for microstructural properties explained a larger proportion of variance than did QTL for meat quality and body composition.

Conclusion

Microstructural properties of pig muscle and meat quality are governed by genetic variation at many loci distributed throughout the genome. QTL analysis under both, the line-cross and half-sib model, allows detecting QTL in case of fixation or segregation of the QTL alleles among the founder populations and thus provide comprehensive insight into the genetic variation of the traits under investigation. Genomic regions affecting complex traits of muscularity and meat quality as well as microstructural properties might point to QTL that in first instance affect muscle fibre traits and by this in second instance meat quality. Disentangling complex traits in their constituent phenotypes might facilitate the identification of QTL and the elucidation of the pleiotropic nature of QTL effects.
A dehydration-inducible gene in the truffle Tuber borchii identifies a novel group of dehydrins
Authors: Abba' Simona , Ghignone Stefano , Bonfante Paola
Published: March 2006

Background

The expressed sequence tag M6G10 was originally isolated from a screening for differentially expressed transcripts during the reproductive stage of the white truffle Tuber borchii. mRNA levels for M6G10 increased dramatically during fruiting body maturation compared to the vegetative mycelial stage.

Results

Bioinformatics tools, phylogenetic analysis and expression studies were used to support the hypothesis that this sequence, named TbDHN1, is the first dehydrin (DHN)-like coding gene isolated in fungi. Homologs of this gene, all defined as "coding for hypothetical proteins" in public databases, were exclusively found in ascomycetous fungi and in plants. Although complete (or almost complete) fungal genomes and EST collections of some Basidiomycota and Glomeromycota are already available, DHN-like proteins appear to be represented only in Ascomycota. A new and previously uncharacterized conserved signature pattern was identified and proposed to Uniprot database as the main distinguishing feature of this new group of DHNs. Expression studies provide experimental evidence of a transcript induction of TbDHN1 during cellular dehydration.

Conclusion

Expression pattern and sequence similarities to known plant DHNs indicate that TbDHN1 is the first characterized DHN-like protein in fungi. The high similarity of TbDHN1 with homolog coding sequences implies the existence of a novel fungal/plant group of LEA Class II proteins characterized by a previously undescribed signature pattern.