bluuebunny/crossref_metadata_2025 huggingface dataset:
Regeneration and the need for simpler model organisms
Authors: Alvarado Alejandro Sánchez
Published: May 2004

The problem of regeneration is fundamentally a problem of tissue homeostasis involving the replacement of cells lost to normal ‘wear and tear’ (cell turnover), and/or injury. This attribute is of particular significance to organisms possessing relatively long lifespans, as maintenance of all body parts and their functional integration is essential for their survival. Because tissue replacement is broadly distributed among multicellular life–forms, and the molecules and mechanisms controlling cellular differentiation are considered ancient evolutionary inventions, it should be possible to gain key molecular insights about regenerative processes through the study of simpler animals. We have chosen to study and develop the freshwater planarianSchmidtea mediterraneaas a model system because it is one of the simplest metazoans possessing tissue homeostasis and regeneration, and because it has become relatively easy to molecularly manipulate this organism. The developmental plasticity and longevity ofS.mediterraneais in marked contrast to its better–characterized invertebrate cohorts: the fruitflyDrosophila melanogasterand the roundwormCaenorhabditis elegans, both of which have short lifespans and are poor at regenerating tissues. Therefore, planarians present us with new, experimentally accessible contexts in which to study the molecular actions guiding cell fate restriction, differentiation and patterning, each of which is crucial not only for regeneration to occur, but also for the survival and perpetuation of all multicellular organisms.
Genetic approaches to disease and regeneration
Authors: Keating Mark T.
Published: May 2004

Cardiovascular disease is largely a consequence of coronary artery blockage through excessive proliferation of smooth muscle cells. It in turn leads to myocardial infarction and permanent and functionally devastating tissue damage to the heart wall. Our studies have revealed that elastin is a primary player in maintaining vascular smooth muscle cells in their dormant state and thus may be a useful therapeutic in vascular disease. By studying zebrafish, which unlike humans, can repair damage to heart muscle, we have begun to uncover some of the genes that seem necessary to undertake the de–differentiation steps that currently fail and prevent the formation of new proliferating cardiomyocytes at the site of damage in a mammalian heart.
Retinoic acid in alveolar development, maintenance and regeneration
Authors: Maden Malcolm , Hind Matthew
Published: May 2004

Recent data suggest that exogenous retinoic acid (RA), the biologically active derivative of vitamin A, can induce alveolar regeneration in a rat model of experimental emphysema. Here, we describe a mouse model of disrupted alveolar development using dexamethasone administered postnatally. We show that the effects of dexamethasone are concentration dependent, dose dependent, long lasting and result in a severe loss of alveolar surface area. When RA is administered to these animals as adults, lung architecture and the surface area per unit of body weight are completely restored to normal. This remarkable effect may be because RA is required during normal alveolar development and administering RA re–awakens gene cascades used during development. We provide evidence that RA is required during alveologenesis in the mouse by showing that the levels of the retinoid binding proteins, the RA receptors and two RA synthesizing enzymes peak postnatally. Furthermore, an inhibitor of RA synthesis, disulphiram, disrupts alveologenesis. We also show that RA is required throughout life for the maintenance of lung alveoli because when rats are deprived of dietary retinol they lose alveoli and show the features of emphysema. Alveolar regeneration with RA may therefore be an important novel therapeutic approach to the treatment of respiratory diseases characterized by a reduced gas–exchanging surface area such as bronchopulmonary dysplasia and emphysema for which there are currently no treatments.
Stem cells: cross–talk and developmental programs
Authors: Imitola Jaime , Park Kook In , Teng Yang D. , Nisim Sahar , Lachyankar Mahesh , Ourednik Jitka , Mueller Franz-Josef , Yiou Rene , Atala Anthony , Sidman Richard L. , Tuszynski Mark , Khoury Samia J. , Snyder Evan Y.
Published: May 2004

The thesis advanced in this essay is that stem cells—particularly those in the nervous system—are components in a series of inborn ‘programs’ that not only ensure normal development, but persist throughout life so as to maintain homeostasis in the face of perturbations—both small and great. These programs encode what has come to be called ‘plasticity’. The stem cell is one of the repositories of this plasticity. This review examines the evidence that interaction between the neural stem cell (as a prototypical somatic stem cell) and the developing or injured brain is a dynamic, complex, ongoing reciprocal set of interactions where both entities are constantly in flux. We suggest that this interaction can be viewed almost from a ‘systems biology’ vantage point. We further advance the notion that clones of exogenous stem cells in transplantation paradigms may not only be viewed for their therapeutic potential, but also as biological tools for ‘interrogating’ the normal or abnormal central nervous system environment, indicating what salient cues (among the many present) are actually guiding the expression of these ‘programs’; in other words, using the stem cell as a ‘reporter cell’. Based on this type of analysis, we suggest some of the relevant molecular pathways responsible for this ‘cross–talk’ which, in turn, lead to proliferation, migration, cell genesis, trophic support, protection, guidance, detoxification, rescue, etc. This type of developmental insight, we propose, is required for the development of therapeutic strategies for neurodegenerative disease and other nervous system afflictions in humans. Understanding the relevant molecular pathways of stem cell repair phenotype should be a priority, in our view, for the entire stem cell field.
The Ensembl Automatic Gene Annotation System
Authors: Curwen Val , Eyras Eduardo , Andrews T. Daniel , Clarke Laura , Mongin Emmanuel , Searle Steven M.J. , Clamp Michele
Published: May 2004

As more genomes are sequenced, there is an increasing need for automated first-pass annotation which allows timely access to important genomic information. The Ensembl gene-building system enables fast automated annotation of eukaryotic genomes. It annotates genes based on evidence derived from known protein, cDNA, and EST sequences. The gene-building system rests on top of the core Ensembl (MySQL) database schema and Perl Application Programming Interface (API), and the data generated are accessible through the Ensembl genome browser (http://www.ensembl.org). To date, the Ensembl predicted gene sets are available for the A. gambiae, C. briggsae, zebrafish, mouse, rat, and human genomes and have been heavily relied upon in the publication of the human, mouse, rat, and A. gambiae genome sequence analysis. Here we describe in detail the gene-building system and the algorithms involved. All code and data are freely available from http://www.ensembl.org.
The Ensembl Analysis Pipeline
Authors: Potter Simon C. , Clarke Laura , Curwen Val , Keenan Stephen , Mongin Emmanuel , Searle Stephen M.J. , Stabenau Arne , Storey Roy , Clamp Michele
Published: May 2004

The Ensembl pipeline is an extension to the Ensembl system which allows automated annotation of genomic sequence. The software comprises two parts. First, there is a set of Perl modules (“Runnables” and “RunnableDBs”) which are `wrappers' for a variety of commonly used analysis tools. These retrieve sequence data from a relational database, run the analysis, and write the results back to the database. They inherit from a common interface, which simplifies the writing of new wrapper modules. On top of this sits a job submission system (the “RuleManager”) which allows efficient and reliable submission of large numbers of jobs to a compute farm. Here we describe the fundamental software components of the pipeline, and we also highlight some features of the Sanger installation which were necessary to enable the pipeline to scale to whole-genome analysis.
ESTGenes: Alternative Splicing From ESTs in Ensembl
Authors: Eyras Eduardo , Caccamo Mario , Curwen Val , Clamp Michele
Published: May 2004

We describe a novel algorithm for deriving the minimal set of nonredundant transcripts compatible with the splicing structure of a set of ESTs mapped on a genome. Sets of ESTs with compatible splicing are represented by a special type of graph. We describe the algorithms for building the graphs and for deriving the minimal set of transcripts from the graphs that are compatible with the evidence. These algorithms are part of the Ensembl automatic gene annotation system, and its results, using ESTs, are provided at www.ensembl.org as ESTgenes for the mosquito, Caenorhabditis briggsae, C. elegans, zebrafish, human, mouse, and rat genomes. Here we also report on the results of this method applied to the human and mouse genomes.
The Ensembl Web Site: Mechanics of a Genome Browser
Authors: Stalker James , Gibbins Brian , Meidl Patrick , Smith James , Spooner William , Hotz Hans-Rudolf , Cox Antony V.
Published: May 2004

The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (∼2.5 million hits) per week, providing access to >80 GB (gigabyte) of data to users in more than 80 countries. Built atop an open-source platform comprising Apache/mod_perl and the MySQL relational database management system, it is modular, extensible, and freely available. It is being actively reused and extended in several different projects, and has been downloaded and installed in companies and academic institutions worldwide. Here, we describe some of the technical features of the site, with particular reference to its dynamic configuration that enables it to handle disparate data from multiple species.
GeneWise and Genomewise
Authors: Birney Ewan , Clamp Michele , Durbin Richard
Published: May 2004

We present two algorithms in this paper: GeneWise, which predicts gene structure using similar protein sequences, and Genomewise, which provides a gene structure final parse across cDNA- and EST-defined spliced structure. Both algorithms are heavily used by the Ensembl annotation system. The GeneWise algorithm was developed from a principled combination of hidden Markov models (HMMs). Both algorithms are highly accurate and can provide both accurate and complete gene structures when used with the correct evidence.
The Ensembl Computing Architecture
Authors: Cuff James A. , Coates Guy M.P. , Cutts Tim J.R. , Rae Mark
Published: May 2004

Ensembl is a software project to automatically annotate large eukaryotic genomes and release them freely into the public domain. The project currently automatically annotates 10 complete genomes. This makes very large demands on compute resources, due to the vast number of sequence comparisons that need to be executed. To circumvent the financial outlay often associated with classical supercomputing environments, farms of multiple, lower-cost machines have now become the norm and have been deployed successfully with this project. The architecture and design of farms containing hundreds of compute nodes is complex and nontrivial to implement. This study will define and explain some of the essential elements to consider when designing such systems. Server architecture and network infrastructure are discussed with a particular emphasis on solutions that worked and those that did not (often with fairly spectacular consequences). The aim of the study is to give the reader, who may be implementing a large-scale biocompute project, an insight into some of the pitfalls that may be waiting ahead.
Sockeye: A 3D Environment for Comparative Genomics
Authors: Montgomery Stephen B. , Astakhova Tamara , Bilenky Mikhail , Birney Ewan , Fu Tony , Hassel Maik , Melsopp Craig , Rak Marcin , Robertson A. Gordon , Sleumer Monica , Siddiqui Asim S. , Jones Steven J.M.
Published: May 2004

Comparative genomics techniques are used in bioinformatics analyses to identify the structural and functional properties of DNA sequences. As the amount of available sequence data steadily increases, the ability to perform large-scale comparative analyses has become increasingly relevant. In addition, the growing complexity of genomic feature annotation means that new approaches to genomic visualization need to be explored. We have developed a Java-based application called Sockeye that uses three-dimensional (3D) graphics technology to facilitate the visualization of annotation and conservation across multiple sequences. This software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization.
Testing the Chromosomal Speciation Hypothesis for Humans and Chimpanzees
Authors: Zhang Jianzhi , Wang Xiaoxia , Podlaha Ondrej
Published: May 2004

Fixed differences of chromosomal rearrangements between isolated populations may promote speciation by preventing between-population gene flow upon secondary contact, either because hybrids suffer from lowered fitness or, more likely, because recombination is reduced in rearranged chromosomal regions. This chromosomal speciation hypothesis thus predicts more rapid genetic divergence on rearranged than on colinear chromosomes because the former are less porous to gene flow. A number of studies of fungi, plants, and animals, including limited genetic data of humans and chimpanzees, support the hypothesis. Here we reexamine the hypothesis for humans and chimpanzees with substantially more genomic data than were used previously. No difference is observed between rearranged and colinear chromosomes in the level of genomic DNA sequence divergence between species. The same is also true for protein sequences. When the gorilla is used as an outgroup, no acceleration in protein sequence evolution associated with chromosomal rearrangements is found. Furthermore, divergence in expression pattern between orthologous genes is not significantly different for rearranged and colinear chromosomes. These results, showing that chromosomal rearrangements did not affect the rate of genetic divergence between humans and chimpanzees, are expected if incipient species on the evolutionary lineages separating humans and chimpanzees did not hybridize.
A Versatile Assay for High-Throughput Gene Expression Profiling on Universal Array Matrices
Authors: Fan Jian-Bing , Yeakley Joanne M. , Bibikova Marina , Chudin Eugene , Wickham Eliza , Chen Jing , Doucet Dennis , Rigault Philippe , Zhang Baohong , Shen Richard , McBride Celeste , Li Hai-Ri , Fu Xiang-Dong , Oliphant Arnold , Barker David L. , Chee Mark S.
Published: May 2004

We report a flexible, sensitive, and quantitative gene-expression profiling system for assaying more than 400 genes, with three probes per gene, for 96 samples in parallel. The cDNA-mediatedannealing,selection, extension andligation (DASL) assay targets specific transcripts, using oligonucleotides containing unique address sequences that can hybridize to universal arrays. Cell-specific gene expression profiles were obtained using this assay for hormone-treated cell lines and laser-capture microdissected cancer tissues. Gene expression profiles derived from this assay were consistent with those determined by qRT-PCR. The DASL assay has been automated for use with a bead-based 96-array matrix system. The combined high-throughput assay and readout system is accurate and efficient, and can cost-effectively profile the expression of hundreds of genes in thousands of samples.
Dynamics of a Human Interparalog Gene Conversion Hotspot
Authors: Bosch Elena , Hurles Matthew E. , Navarro Arcadi , Jobling Mark A.
Published: May 2004

Gene conversion between paralogs can alter their patterns of sequence identity, thus obscuring their evolutionary relationships and affecting their propensity to sponsor genomic rearrangements. The details of this important process are poorly understood in the human genome because allelic diversity complicates the interpretation of interparalog sequence differences. Here we exploit the haploid nature of the Y chromosome, which obviates complicating interallelic processes, together with its known phylogeny, to understand the dynamics of conversion between two directly repeated HERVs flanking the 780-kb AZFa region on Yq. Sequence analysis of a 787-bp segment of each of the HERVs in 36 Y chromosomes revealed one of the highest nucleotide diversities in the human genome, as well as evidence of a complex patchwork of highly directional gene conversion events. The rate of proximal-to-distal conversion events was estimated as 2.4 × 10-4 to 1.2 × 10-3 per generation (3.9 × 10-7 to 1.9 × 10-6 per base per generation), and the distal-to-proximal rate as about one-twentieth of this. Minimum observed conversion tract lengths ranged from 1 to 158 bp and maximum lengths from 19 to 1365 bp, with an estimated mean of 31 bp. Analysis of great ape homologs shows that conversion in this hotspot has a deep evolutionary history.
The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint
Authors: Castillo-Davis Cristian I. , Kondrashov Fyodor A. , Hartl Daniel L. , Kulathinal Rob J.
Published: May 2004

We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biological requirements; and (2) rates of divergence are distributed differently among functional classes within each lineage, indicating species-specific selective regimes impact genome-wide substitutional patterns. Integrating comparative genome sequence with data from tissue-specific expressed-sequence-tag (EST) libraries and detailed database annotations, we find a functional genomic signature of rapid evolution and selective constraint shared between mammalian and nematode lineages despite their extensive morphological and ecological differences and distant common ancestry. In both phyla, we find evidence of accelerated evolution among components of molecular systems involved in coevolutionary change. In mammals, lineage-specific fast evolving genes include those involved in reproduction, immunity, and possibly, maternal–fetal conflict. Likelihood ratio tests provide evidence for positive selection in these rapidly evolving functional categories in mammals. In contrast, slowly evolving genes, in terms of amino acid or insertion/deletion (indel) change, in both phyla are involved in core molecular processes such as transcription, translation, and protein transport. Thus, strong purifying selection appears to act on the same core cellular processes in both mammalian and nematode lineages, whereas positive and/or relaxed selection acts on different biological processes in each lineage.
The Human MitoChip: A High-Throughput Sequencing Microarray for Mitochondrial Mutation Detection
Authors: Maitra Anirban , Cohen Yoram , Gillespie Susannah E.D. , Mambo Elizabeth , Fukushima Noriyoshi , Hoque Mohammad O. , Shah Nila , Goggins Michael , Califano Joseph , Sidransky David , Chakravarti Aravinda
Published: May 2004

Somatic mitochondrial mutations are common in human cancers, and can be used as a tool for early detection of cancer. We have developed a mitochondrial Custom Reseq™ microarray as an array-based sequencing platform for rapid and high-throughput analysis of mitochondrial DNA. The MitoChip contains oligonucleotide probes synthesized using standard photolithography and solid-phase synthesis, and is able to sequence >29 kb of double-stranded DNA in a single assay. Both strands of the entire human mitochondrial coding sequence (15,451 bp) are arrayed on the MitoChip; both strands of an additional 12,935 bp (84% of coding DNA) are arrayed in duplicate. We used 300 ng of genomic DNA to amplify the mitochondrial coding sequence in three overlapping long PCR fragments. We then sequenced >2 million base pairs of mitochondrial DNA, and successfully assigned base calls at 96.0% of nucleotide positions. Replicate experiments demonstrated >99.99% reproducibility. In matched fluid samples (urine and pancreatic juice, respectively) obtained from five patients with bladder cancer and four with pancreatic cancer, the MitoChip detected at least one cancer-associated mitochondrial mutation in six (66%) of nine samples. The MitoChip is a high-throughput sequencing tool for the reliable identification of mitochondrial DNA mutations from primary tumors in clinical samples.
Analysis of Segmental Duplications and Genome Assembly in the Mouse
Authors: Bailey Jeffrey A. , Church Deanna M. , Ventura Mario , Rocchi Mariano , Eichler Evan E.
Published: May 2004

Limited comparative studies suggest that the human genome is particularly enriched for recent segmental duplications. The extent of segmental duplications in other mammalian genomes is unknown and confounded by methodological differences in genome assembly. Here, we present a detailed analysis of recent duplication content within the mouse genome using a whole-genome assembly comparison method and a novel assembly independent method, designed to take advantage of the reduced allelic variation of the C57BL/6J strain. We conservatively estimate that ∼57% of all highly identical segmental duplications (≥90%) were misassembled or collapsed within the working draft WGS assembly. The WGS approach often leaves duplications fragmented and unassigned to a chromosome when compared with the clone-ordered-based approach. Our preliminary analysis suggests that 1.7%–2.0% of the mouse genome is part of recent large segmental duplications (about half of what is observed for the human genome). We have constructed a mouse segmental duplication database to aid in the characterization of these regions and their integration into the final mouse genome assembly. This work suggests significant biological differences in the architecture of recent segmental duplications between human and mouse. In addition, our unique method provides the means for improving whole-genome shotgun sequence assembly of mouse and future mammalian genomes.
Compositional Gene Landscapes in Vertebrates
Authors: Cruveiller Stéphane , Jabbari Kamel , Clay Oliver , Bernardi Giorgio
Published: May 2004

The existence of a well conserved linear relationship between GC levels of genes' second and third codon positions (GC2, GC3) prompted us to focus on the landscape, or joint distribution, spanned by these two variables. In human, well curated coding sequences now cover at least 15%–30% of the estimated total gene set. Our analysis of the landscape defined by this gene set revealed not only the well documented linear crest, but also the presence of several peaks and valleys along that crest, a property that was also indicated in two other warm-blooded vertebrates represented by large gene databases, that is, mouse and chicken. GC2 is the sum of eight amino acid frequencies, whereas GC3 is linearly related to the GC level of the chromosomal region containing the gene. The landscapes therefore portray relations between proteins and the DNA environments of the genes that encode them.
Research Collaborations with Sequential Investments
Authors: Lülfesmann Christoph
Published: May 2004

The paper investigates research collaborations where one partner performs R&D at an initial stage whereas the second partner subsequently invests in the success of a joint project. We allow for any degree of uncertainty of the project's success. It is shown that exclusive ownership of one partner necessarily triggers suboptimal initial research even if renegotiation is admitted. Conversely, joint ownership in form of an equity joint venture or a contingent ownership structure (an option‐to‐buy arrangement) may facilitate an efficient outcome. In equilibrium, the initially chosen governance structure is always renegotiated which conforms well with empirical evidence.
Job Tenure in Britain: Employee Characteristics versus Workplace Effects
Authors: Mumford Karen , Smith Peter N.
Published: May 2004

We consider differences in current job tenure of individuals using linked employee and workplace data. This enables us to distinguish between variation in tenure associated with the characteristics of individual employees and those of the workplace in which they work. As a group, The various individual characteristics are found to be essentially uncorrelated with the workplace effect. However, this is not true for women and non‐white employees; we find that the lower tenure associated with membership of these demographic groups is captured predominantly by workplace effects, suggesting some degree of labour market segmentation in Britain.
The Demand for Insurance With an Upper Limit on Coverage
Authors: Cummins J. David , Mahul Olivier
Published: May 2004

Abstract

The demand for insurance is examined when the indemnity schedule is subject to an upper limit. The optimal contract is shown to display full insurance above a deductible up to the cap. Some results derived in the standard model with no upper limit on coverage turn out to be invalid; the optimal deductible of an actuarially fair policy is positive and insurance may be a normal good under decreasing absolute risk aversion. An increase in the upper limit would induce the policyholder with constant absolute risk aversion to reduce his or her optimal deductible and therefore this would increase the demand for insurance against small losses.
A Data‐Analytic Method for Forecasting Next Record Catastrophe Loss
Authors: Hsieh Ping‐Hung
Published: May 2004

Abstract

We develop in this article a data‐analytic method to forecast the severity of next record insured loss to property caused by natural catastrophic events. The method requires and employs the knowledge of an expert and accounts for uncertainty in parameter estimation. Both considerations are essential for the task at hand because the available data are typically scarce in extreme value analysis. In addition, we consider three‐parameter Gamma priors for the parameter in the model and thus provide simple analytical solutions to several key elements of interest, such as the predictive moments of record value. As a result, the model enables practitioners to gain insights into the behavior of such predictive moments without concerning themselves with the computational issues that are often associated with a complex Bayesian analysis. A data set consisting of catastrophe losses occurring in the United States between 1990 and 1999 is analyzed, and the forecasts of next record loss are made under various prior assumptions. We demonstrate that the proposed method provides more reliable and theoretically sound forecasts, whereas the conditional mean approach, which does not account for either prior information or uncertainty in parameter estimation, may provide inadmissible forecasts.
Malassezia Enhances Natural Killer Cell‐Induced Dendritic Cell Maturation
Authors: Buentke E. , D'Amato M. , Scheynius A.
Published: May 2004

Human natural killer (NK) cells can induce cell death in autologous dendritic cells (DCs), though an interaction between these two cell types can also lead to a reciprocal activation. We have recently shown cell contact between NK cells and DCs in vivo, in Malassezia‐induced lesional skin of patients with atopic eczema, where the yeast acts as an allergen although it is part of the normal skin microflora. Here we characterize the interaction of human NK cells and monocyte‐derived DCs (MDDCs) by using an in vitro system where short‐term activated polyclonal NK cells are cocultured with autologous, immature, Malassezia‐stimulated or lipopolysaccharide‐matured MDDCs. We found that the number of CD83+ MDDCs increased in the immature and Malassezia‐stimulated MDDCs upon coculture with NK cells, while an increased number of CD86+ cells was detected in the Malassezia‐stimulated MDDCs. NK cell–MDDC interaction induced the production of interleukin‐8 (IL‐8). In conclusion, our results imply that NK cells provide maturation signals and may play a role in inducing IL‐8 production in DCs. Furthermore, the increased expression of CD86 on Malassezia‐stimulated MDDCs might have a function in subsequent T‐cell activation by DCs, and indicate a role for NK cell–DC interaction in modulating the immune responses to microbial stimuli.
Chicken B‐Cell‐Activating Factor: Regulator of B‐Cell Survival in the Bursa of Fabricius
Authors: Koskela K. , Nieminen P. , Kohonen P. , Salminen H. , Lassila O.
Published: May 2004

Previous studies on mammals have demonstrated that a tumour necrosis factor family member, B‐cell‐activating factor (BAFF) (BlyS, TALL‐1), is mainly produced by myeloid and dendritic cells and that BAFF promotes B‐cell differentiation and survival in a paracrine fashion. We have recently shown that BAFF is upregulated at the bursal stage of the avian B‐cell development. We now show that the avian bursal B cells and B‐cell lines, RP‐9, RP‐13 and DT40, express chicken BAFF (cBAFF). In situ hybridization confirms strong cBAFF expression within the bursal follicles. Like mammals, cBAFF is expressed in the avian myeloblast and myelomonocytic cell lines but not in the peripheral blood αβ and γδ T cells. The binding of recombinant human BAFF (hBAFF) to the bursal B‐cells indicates a conserved receptor–ligand binding. Furthermore, the recombinant hBAFF has a positive effect on bursal cell proliferation and transiently inhibits cell death in vitro. In conclusion, cBAFF is highly conserved structurally, but as a novel observation we suggest cBAFF to function in an autocrine fashion to promote the growth and maturation of follicular B cells in bursa of Fabricius.
Induction of a Mucosal Immune Response to the Streptococcal M Protein by Intramuscular Administration of a PADRE‐ASREAK Peptide
Authors: Pamonsinlapatham P. , Decroix N. , Mihaila‐Amrouche L. , Bouvet A. , Bouvet J.‐P.
Published: May 2004

In a previous study, it was shown that an intramuscular administration of amino acid PADRE‐ELDKWA sequence induced a mucosal immune response to a conserved epitope of human immunodeficiency virus in mice. In the same model, here it is shown that this method can be used with a selected peptide from the M protein of group A streptococci. The PADRE‐ASREAK sequence was injected in mice by the intramuscular route. Antibodies against M protein were detected in extracts of mucosal tissues and in serum. The repertoire isotypes of serum immunoglobulin G (IgG) and mucosal IgA and IgG antibodies varied, according to the dose of injected peptide. The highest mucosal IgA antibody response was obtained with 0.01 µg of antigen per injection, whereas the systemic IgG antibody response increased with 10 µg of antigen. Mucosal antibody production against streptococci was confirmed by immunofluorescence analysis. These results provide evidence that this novel approach of mucosal vaccination may be of advantage for bacterial systems and suggest a new field of investigation based on synthetic peptide analogues.
Alteration of an Autoantigen by Chlorination, a Process Occurring During Inflammation, Can Overcome Adaptive Immune Tolerance
Authors: Westman E. , Harris H. E.
Published: May 2004

Autoimmune diseases are characterized by chronic inflammation in target organs and immunoreactivity towards one or multiple autoantigens. Several potential mechanisms of tolerance breaking have been postulated, one being inflammation‐associated events. We have investigated whether chlorination of an autoantigen can lead to disruption of self‐tolerance. Chlorination of antigens might occur during inflammation via the granulocyte‐specific, myeloperoxidase‐catalysed conversion of hydrogen peroxide to hypochlorous acid (HOCl). HOCl, being a strong oxidant, reacts with proteins both within cellular phagosomes and in the immediate extracellular environment. By immunizing Lew.1AV1 rats with chlorinated or unmodified rat serum albumin (RSA), we could detect tolerance‐breaking effects of chlorination. RSA is a systemic autoantigen in rat not inducing antibody production upon immunization in its unmodified form. Rats immunized with chlorinated RSA (RSA‐Cl) developed high titres of immunoglobulin G (IgG) specific for RSA‐Cl which cross‐reacted with native RSA. T cells reactive with both RSA‐Cl and RSA were detected by [3H]‐thymidine incorporation. We hence speculated that immunological tolerance established for unmodified proteins, during certain circumstances such as inflammation, might be broken by induced protein chlorination. T cells specific for the chlorinated protein can confer help to B cells recognizing both the chlorinated and the native form of the protein, leading to the formation of high‐affinity autoreactive antibodies and possibly autoimmune disease.
Feature: Implications of climate change for hazardous ground conditions in the UK
Authors: Forster Alan , Culshaw Martin
Published: May 2004

Many geohazards affect the United Kingdom, both directly and indirectly. As climate might change in the future, it may affect the geohazards that we, and our descendents, will have to face as a consequence of those changes.
Expression of SPANX proteins in human‐ejaculated spermatozoa and sperm precursors
Authors: Salemi Michele , Calogero Aldo E. , Benedetto Daniela Di , Cosentino Anna , Barone Nunziata , Rappazzo Giancarlo , Vicari Enzo
Published: May 2004

The sperm protein associated with nucleus in the X chromosome (SPANX) gene family is constituted by only a few members, clustered at Xq27, encoding small proteins which range from 15 to 20 kDa. These proteins have been shown to be present both in mature spermatozoa and in tumours, such as melanoma and some leukaemias. We developed polyclonal sera in order to study the distribution of the protein in human‐ejaculated spermatozoa and their precursors. A synthetic peptide was designed from a domain common to the SPANX protein family and polyclonal sera were raised in mice. Seven healthy volunteer men with normal sperm parameters were recruited and the expression of SPANX proteins was evaluated in spermatozoa and ejaculated sperm precursors by immunocytochemistry and immunofluorescence analyses. SPANX proteins, present in a large fraction (96%) of mature spermatozoa, were localized in the sperm head (39.2%), midpiece (22.8%) or in both sites (34.4%). Spermatids also showed the presence of SPANX proteins in their cytoplasm, although a significantly higher number of spermatids were SPANX‐negative compared with spermatozoa. In conclusion, SPANX proteins are expressed in an elevated percentage of spermatids and mature spermatozoa. In the latter, they are preferentially located in the sperm head. The greater number of SPANX‐negative spermatids observed could relate to their easier exfoliation from the seminiferous tubules.
The neutral comet assay detects double strand DNA damage in selected and unselected human spermatozoa of normospermic donors
Authors: Van Kooij R. J. , De Boer P. , De Vreeden‐Elbertse J. M. T. , Ganga N. A. , Singh N. , Te Velde E. R.
Published: May 2004

The occurrence of DNA breaks in human sperm is of concern to genetic safety in artificial reproduction techniques. Here, we have explored the neutral comet assay (NCA) for evaluating the frequency of spermatozoa with double strand (ds) DNA breaks in normospermic donors. The NCA results into DNA tail formation by fibre extension and by the separation of DNA fragments. Gamma‐irradiated native, lysed and lysed plus RNA and protein degraded human sperm nuclei have been used to assess sensitivity and specificity of fragment formation as an indication for ds DNA breaks. At 5 and 10 Gy gamma irradiation, the sensitivity increases in the order: native, lysed, lysed plus RNA and protein degraded. At 10 Gy, a uniform response between donors was obtained. For technical and biological reasons, the NCA underestimates the true incidence of ds DNA breaks by an unknown factor. Semen samples of six healthy normospermic donors were differentiated by swim up and by Percoll density centrifugation, followed by the NCA. In native semen, percentages of sperm nuclei with ds DNA breaks ranged from 15 to 25%. Swim up and selection for high‐density sperm nuclei (high Percoll fraction) reduced the frequency of sperm with ds DNA breaks by about one third, whereas an increased frequency was found in the low Percoll fraction. In conclusion, the response to gamma irradiation of DNA fragment formation indicates the NCA to demonstrate ds DNA breaks which is in keeping with theory and experimental results from somatic cells. Ds DNA breaks are a characteristic of the sperm population of normal donors. Current sperm selection procedures reduce the fractions of sperm with ds DNA breaks, yet are not effective in eliminating these cells.
Cloning and characterization of a mouse spergen‐1 localized in sperm mitochondria
Authors: Matsuoka Yasuhiro , Iguchi Naoko , Kitamura Kouichi , Nishimura Hiromi , Manabe Hiroyuki , Miyagawa Yasushi , Koga Minoru , Matsumiya Kiyomi , Okuyama Akihiko , Tanaka Hiromitsu , Nishimune Yoshitake
Published: May 2004

Development of spermatozoa is a complex process involving specific morphological formation of flagella, nucleus and mitochondria. Although detailed morphological observations of these events are available, the molecular mechanisms remain to be fully elucidated. We report here the molecular cloning and characterization of mouse spergen‐1 encoding a sperm specific mitochondrial protein, from a haploid germ cell‐specific subtracted cDNA library of mouse testis. Isolated cDNA is c. 0.7 kb and contains a 465 bp ORF that encodes mouse spergen‐1, a sperm mitochondrial protein consisting of 154 predicted amino acids. Antibodies raised against mouse Spergen‐1 identified a testis‐specific c. 18 Mr × 103 band in Western blot analysis. The protein was localized to the mitochondria of mouse sperm. Comparison of the mouse and human genomic sequences showed that 55 bps of the 5′‐upstream region containing a CAAT box and binding sequence for NF‐κB is conserved and could be important for specific expression of mouse spergen‐1 in haploid germ cells.
Expression of the apoptosis inhibitor survivin in testicular tissue of infertile patients
Authors: Weikert Steffen , Schrader Mark , Müller Markus , Krause Hans , Miller Kurt
Published: May 2004

Apoptosis is a common phenomenon during spermatogenesis, and its dysregulation has been associated with male infertility. Survivin is an inhibitor of apoptosis protein that regulates apoptosis at cell division and is overexpressed in common human cancers. We investigated whether survivin mRNA expression is detectable in testicular biopsies from patients with infertility of varying aetiology. The aim of this study was to examine the testicular survivin expression in azoospermic men with normal spermatogenesis and in those with specific spermatogenic disorders. Survivin mRNA expression was detected by reverse transcriptase‐polymerase chain reaction in histologically classified testicular biopsy specimens from 30 azoospermic men. Survivin was found to be expressed in normal spermatogenesis (n = 10), in post‐meiotic spermatogenic arrest (n = 6), and in specimens showing a mixed picture of pre‐meiotic maturation arrest with sparse islands of post‐meiotic arrest (n = 2). In contrast, a lack of survivin expression was seen in specimens without haploid germ cells (pre‐meiotic maturation arrest, n = 2) and in those with Sertoli‐cell‐only syndrome (SCOS, n = 10). These data indicate for the first time that survivin is expressed in human testis. Moreover, its expression seems to correlate with the stage of maturation arrest in patients presenting with spermatogenic disorders. Survivin mRNA expression was not found in SCOS specimens, possibly indicating germ‐cell‐specific expression in human testicular tissue. Thus, survivin is a potential molecular marker of spermatogenesis, whose expression is altered in specific spermatogenic disorders.
Putative biological functions of the DAZ family
Authors: Yen Pauline H.
Published: May 2004

The Deleted in Azoospermia (DAZ) gene belongs to a gene family that consists of three members: BOULE, DAZ‐Like (DAZL) and DAZ. Members of the DAZ family are expressed exclusively in the germ cells, and their protein products contain a highly conserved RNA‐binding motif and a unique DAZ repeat. Null mutations of the DAZ family members affect the fertility of either male or female, or both sexes. DAZ and DAZL are expressed throughout most of the life of germ cells and are required for the development of primordial germ cells and the differentiation and maturation of the germ cells. BOULE is expressed around the time of meiosis and has a more limited function. The DAZ proteins bind to RNAs in vitro and in vivo and are probably involved in the post‐transcriptional regulation of mRNA expression. Their downstream RNA targets remain largely unknown, although members of the CDC25 gene family are potential candidates.
Chromosomal abnormalities in couples undergoing intracytoplasmic sperm injection. A study of 370 couples and review of the literature
Authors: Morel F. , Douet‐Guilbert N. , Le Bris M.‐J. , Amice V. , Le Martelot M. T. , Roche S. , Valéri A. , Derrien V. , Amice J. , De Braekeleer M.
Published: May 2004

Intracytoplasmic sperm injection (ICSI) is now widely acknowledged as the most effective therapeutic approach to severe male infertility or unsuccessful in vitro fertilization. Cytogenetic investigations were performed in 370 females and 335 males prior to ICSI between January 1997 and April 2003. Nine men (2.7%) and 48 women (13%) had an abnormal karyotype, 44 females having some degree of numerical sex chromosome mosaicism. A review of the literature showed the prevalence of all types of chromosomal abnormalities to be much higher among male and female partners of couples examined prior to ICSI than among newborns. As most ICSIs are performed with ejaculated spermatozoa from oligospermic men, the distribution and the prevalence of the several types of chromosomal abnormalities are closer to those of oligospermic rather than azoospermic males. Our results combined with those of the literature stress the importance of karyotyping both male and female partners before ICSI is started. Adequate genetic counselling, possibly followed by prenatal diagnosis, should be offered if a chromosomal anomaly is detected.
Nursing ethics and conceptualizations of nursing: profession, practice and work
Authors: Liaschenko Joan , Peter Elizabeth
Published: May 2004

Background. Nursing has been understood as a calling, vocation, profession, and most recently, a practice. Each of these conceptualizations has associated with it an ethics that has emphasized particular aspects of nursing reflecting the social position of nursing in a given historical period. The ethics associated with current understandings of nursing as a profession and a practice are, we believe, no longer adequate to address the social realities and moral challenges of health care work.

Aim. The aim of this paper is to discuss the limitations of the ethics associated with profession and practice and to show why the concept of work can contribute to a nursing ethics.

Discussion. The characteristics that have socially defined professionals, among them the possession of a unique body of knowledge, provision of an altruistic service to society, and autonomy in the sense of control over their work and work conditions, only partially reflect the realities of contemporary health care work. This is true even for physicians, an exemplar of a professional group. The ethics associated with the professions has tended to limit what counts as a moral concern and who is authorized to label them as such. More recently, the idea of a practice has been used to argue for an ethics in which professional activities of a certain kind and understood in a specific way are inherently moral. However, this approach is limited for similar reasons. Because morality cannot be separated from the social organization of health care, we argue that considering nursing primarily as work, in contrast to a profession or a practice, offers the possibility of an ethics that more completely reflects the complexity of contemporary health care.

Conclusion. Beyond the obvious conclusion that nursing is work, conceptualizing nursing as work points to changing social realities that are raising significant ethical issues. As a concept, work inherently conveys value, connects intellectual and manual labour, and recognizes social divisions of labour. At the moment an ethics of work is merely an idea, but we believe that such an ethics would lead nurses to ask different questions and propose different answers to the moral challenges of the present and near future.
Occupational stress and constructive thinking: health and job satisfaction
Authors: Stacciarini Jeanne‐Marie R. , Tróccoli Bartholomeu Torres
Published: May 2004

Background. Occupational stress is associated with specific situations, characteristics of the work environment, and individual perceptions and reactions in the context of the workplace, but many nursing studies of occupational stress have tended to analyse aspects related to the job itself. In Brazil nursing is acknowledged as a stressful occupation whose stresses are generally associated with the job itself, while the effects of personal characteristics on an individual's response to occupational stress are dismissed.

Aims. The aim of this paper is to describe: (1) occupational stress, job satisfaction and state of health in Brazilian nurses, and (2) the relationship of these variables to a constructive thinking coping style.

Methods. A correlational study was performed during 1999 with 461 nurses recruited from the public health and education system in the Federal District of Brazil. Instruments used were the Nursing Stress Inventory, Constructive Thinking Inventory, subscales of the Occupational Stress Indicator, and a researcher‐designed questionnaire.

Results. Normal distributions were found for occupational stress, state of health (physical and psychological), and job satisfaction. Results suggest that nurses have fewer psychological health problems and similar job satisfaction compared with other Brazilian government white‐collar workers. Occupational stress was directly associated with state of health, and inversely associated with global constructive thinking and job satisfaction.

Conclusions. Brazilian nurses in this study seem to have adapted satisfactorily to their profession, but the finding that constructive thinking was significantly related to psychological ill‐health, occupational stress and physical ill‐health highlights a need to value individual coping styles in the work environment.