Multiple DNA and protein sequence alignment based on segment-to-segment comparison.

In this paper, a new way to think about, and to construct, pairwise as well as multiple alignments of DNA and protein sequences is proposed. Rather than forcing alignments to either align single residues or to introduce gaps by defining an alignment as a path running right from the source up to the sink in the associated dot-matrix diagram, we propose to consider alignments as consistent equivalence relations defined on the set of all positions occurring in all sequences under consideration. We also propose constructing alignments from whole segments exhibiting highly significant overall similarity rather than by aligning individual residues. Consequently, we present an alignment algorithm that (i) is based on segment-to-segment comparison instead of the commonly used residue-to-residue comparison and which (ii) avoids the well-known difficulties concerning the choice of appropriate gap penalties: gaps are not treated explicity, but remain as those parts of the sequences that do not belong to any of the aligned segments. Finally, we discuss the application of our algorithm to two test examples and compare it with commonly used alignment methods. As a first example, we aligned a set of 11 DNA sequences coding for functional helix-loop-helix proteins. Though the sequences show only low overall similarity, our program correctly aligned all of the 11 functional sites, which was a unique result among the methods tested. As a by-product, the reading frames of the sequences were identified. Next, we aligned a set of ribonuclease H proteins and compared our results with alignments produced by other programs as reported by McClure et al. [McClure, M. A., Vasi, T. K. & Fitch, W. M. (1994) Mol. Biol. Evol. 11, 571-592]. Our program was one of the best scoring programs. However, in contrast to other methods, our protein alignments are independent of user-defined parameters.

Development of a bovine X chromosome linkage group and painting probes to assess cattle, sheep, and goat X chromosome segment homologies.

The X chromosome linkage group is conserved in placental mammals. However, X chromosome morphological differences, due to internal chromosome rearrangements, exist among mammalian species. We have developed bovine chromosome painting probes for Xp and Xq to assess segment homologies between the submetacentric bovine X chromosome and the acrocentric sheep and goat X chromosomes. These painting probes and their corresponding DNA libraries were developed by chromosome micromanipulation, DNA micropurification, microcloning, and PCR amplification. The bovine Xp painting probe identified an interstitially located homologous segment in the sheep and goat Xq region, most probably resulting from chromosome inversion. Ten type II (microsatellite) markers obtained from the bovine Xq library and five other X chromosome assigned, but unlinked, markers were used to generate a linkage map for Xq spanning 89.4 centimorgans. The chromosome painting probes and molecular markers generated in this study would be useful for comparative mapping and tracing of internal X chromosome rearrangements in all ruminant species and would contribute to the understanding of mammalian sex chromosome evolution.

A de novo missense mutation of the beta subunit of the epithelial sodium channel causes hypertension and Liddle syndrome, identifying a proline-rich segment critical for regulation of channel activity.

Liddle syndrome is a mendelian form of hypertension characterized by constitutively elevated renal Na reabsorption that can result from activating mutations in the beta or gamma subunit of the epithelial Na channel. All reported mutations have deleted the last 45-76 normal amino acids from the cytoplasmic C terminus of one of these channel subunits. While these findings implicate these terminal segments in the normal negative regulation of channel activity, they do not identify the amino acid residues that are critical targets for these mutations. Potential targets include the short highly conserved Pro-rich segments present in the C terminus of beta and gamma subunits; these segments are similar to SH3-binding domains that mediate protein-protein interaction. We now report a kindred with Liddle syndrome in which affected patients have a mutation in codon 616 of the beta subunit resulting in substitution of a Leu for one of these highly conserved Pro residues. The functional significance of this mutation is demonstrated both by the finding that this is a de novo mutation appearing concordantly with the appearance of Liddle syndrome in the kindred and also by the marked activation of amiloride-sensitive Na channel activity seen in Xenopus oocytes expressing channels containing this mutant subunit (8.8-fold increase compared with control oocytes expressing normal channel subunits; P = 0.003). These findings demonstrate a de novo missense mutation causing Liddle syndrome and identify a critical channel residue important for the normal regulation of Na reabsorption in humans.

Invariant chain made in Escherichia coli has an exposed N-terminal segment that blocks antigen binding to HLA-DR1 and a trimeric C-terminal segment that binds empty HLA-DR1.

Invariant chain (Ii), a membrane glycoprotein, binds class II major histocompatibility complex (MHC) glycoproteins, probably via its class II-associated Ii peptide (CLIP) segment, and escorts them toward antigen-containing endosomal compartments. We find that a soluble, trimeric ectodomain of Ii expressed and purified from Escherichia coli blocks peptide binding to soluble HLA-DR1. Proteolysis indicates that Ii contains two structural domains. The C-terminal two-thirds forms an alpha-helical domain that trimerizes and interacts with empty HLA-DR1 molecules, augmenting rather than blocking peptide binding. The N-terminal one-third, which inhibits peptide binding, is proteolytically susceptible over its entire length. In the trimer, the N-terminal domains act independently with each CLIP segment exposed and free to bind an MHC class II molecule, while the C-terminal domains act as a trimeric unit.

Expression of PTPH1, a rat protein tyrosine phosphatase, is restricted to the derivatives of a specific diencephalic segment.

Studies to date have identified only a few proteins that are expressed in a segment-specific manner within the mammalian brain. Here we report that a nonreceptor protein tyrosine phosphatase, PTPH1, is selectively expressed in the adult thalamus. Expression of PTPH1 mRNA is detected in most, but not all, thalamic nuclei. Nuclei that are derived embryonically from the dorsal thalamus and project to the neocortex express this gene, whereas those derived from the ventral thalamus do not. PTPH1 mRNA expression is also restricted to the dorsal thalamus during development and, thus, can serve as a specific marker for the dorsal thalamic nuclei. Since the subcellular localization of PTPH1 protein is not known, its functional role is not clear. However, the restriction of its expression to the thalamic nuclei that have thalamocortical connections suggests that PTPH1 may play a role in the maintenance of these connections or in determining the physiological properties of thalamic relay nuclei.

Binding of the transcription activator NRI (NTRC) to a supercoiled DNA segment imitates association with the natural enhancer: an electron microscopic investigation.

Electron microscopic visualization indicates that the transcription activator NRI (NTRC) binds with exceptional selectivity and efficiency to a sequence-induced superhelical (spiral) segment inserted upstream of the glnA promoter, accounting for its observed ability to substitute for the natural glnA enhancer. The cooperative binding of NRI to the spiral insert leads to protein oligomerization which, at higher concentration, promotes selective coating of the entire superhelical segment with protein. Localization of NRI at apical loops is observed with negatively supercoiled plasmid DNA. With a linear plasmid, bending of DNA is observed. We confirm that NRI is a DNA-bending protein, consistent with its high affinity for spiral DNA. These results prove that spiral DNA without any homology to the NRI-binding sequence site can substitute for the glnA enhancer by promoting cooperative activator binding to DNA and facilitating protein oligomerization. Similar mechanisms might apply to other prokaryotic and eukaryotic activator proteins that share the ability to bend DNA and act efficiently as multimers.

Gender-sensitive reporting in medical research

Sex and gender differences influence the health and wellbeing of men and women. Although studies have drawn attention to observed differences between women and men across diseases, remarkably little research has been pursued to systematically investigate these underlying sex differences. Women continue to be underrepresented in clinical trials, and even in studies in which both men and women participate, systematic analysis of data to identify potential sex-based differences is lacking. Standards for reporting of clinical trials have been established to ensure provision of complete, transparent and critical information. An important step in addressing the gender imbalance would be inclusion of a gender perspective in the next Consolidated Standards of Reporting Trials (CONSORT) guideline revision. Uniform Requirements for Manuscripts Submitted to Biomedical Journals, as a set of well-recognized and widely used guidelines for authors and biomedical journals, should similarly emphasize the ethical obligation of authors to present data analyzed by gender as a matter of routine. Journal editors are also promoters of ethical research and adequate standards of reporting, and requirements for inclusion of gender analyses should be integrated into editorial policies as a matter of urgency.

Technologies for Anatomical and Geometric Characterization of the Corneal Structure and Anterior Segment: A Review

Corneal and anterior segment imaging techniques have become a crucial tool in the clinical practice of ophthalmology, with a great variety of applications, such as corneal curvature and pachymetric analysis, detection of ectatic corneal conditions, anatomical study of the anterior segment prior to phakic intraocular lens implantation, or densitometric analysis of the crystalline lens. From the Placido-based systems that allow only a characterization of the geometry of the anterior corneal surface to the Scheimpflug photography-based systems that provide a characterization of the cornea, anterior chamber, and crystalline lens, there is a great variety of devices with the capability of analyzing different anatomical parameters with very high precision. To date, Scheimpflug photography-based systems are the devices providing the more complete analysis of the anterior segment in a non-invasive way. More developments are required in anterior segment imaging technologies in order to improve the analysis of the crystalline lens structure as well as the ocular structures behind the iris in a non-invasive way when the pupil is not dilated.

Factors Associated With Women’s Reporting of Intimate Partner Violence in Spain

In Spain, in 2013, the 20% of women who were murdered by their partner had reported him previously. We analyze the 2011 Spanish-Macrosurvey on Gender Violence to identify and analyze the prevalence of and the principal factors associated with reporting a situation of intimate partner violence (IPV) and the main reasons women cite for not filing such reports, or for subsequently deciding to withdraw their complaint. Overall, 72.8% of women exposed to IPV did not report their aggressor. The most frequent reasons for not reporting were not giving importance to the situation (33.9%), and fear and lack of trust in the reporting process (21.3%). The main reasons for withdrawing the complaint were cessation of the violence (20.0%), and fear and threats (18.2%). The probability of reporting increased among women with young children who were abused, prevalence ratio (95% confidence interval [CI]): 2.14 [1.54, 2.98], and those whose mother was abused, prevalence ratio (95% CI): 2.25 [1.42, 3.57]. Always focusing on the need to protect women who report abuse, it is necessary to promote the availability of and access to legal resources especially among women who use them less: women who do not have children and women who do not have previous family exposure to violence.

Children's Postures While Playing at Computer Workstations

There has been a significant increase in the incidence of musculoskeletal disorders (MSD) and the costs associated with these are predicted to increase as the popularity of computer use increases at home, school and work. Risk factors have been identified in the adult population but little is known about the risk factors for children and youth. Research has demonstrated that they are not immune to this risk and that they are self reporting the same pain as adults. The purpose of the study was to examine children’s postures while working at computer workstations under two conditions. One was at an ergonomically adjusted children’s workstation while the second was at an average adult workstation. A Polhemus Fastrak™ system was used to record the children’s postures and joint and segment angles were quantified. Results of the study showed that children reported more discomfort and effort at the adult workstation. Segment and joint angles showed significant differences through the upper limb at the adult workstation. Of significance was the strategy of shoulder abduction and flexion that the children used in order to place their hand on the mouse. Ulnar deviation was also greater at the adult workstation as was neck extension. All of these factors have been identified in the literature as increasing the risk for injury. A comparison of the children’s posture while playing at the children’s workstation verses the adult workstation, showed that the postural angles assumed by the children at an adult workstation exceeded the Occupational Safety and Health Association (OSHA) recommendations. Further investigation is needed to increase our knowledge of MSD in children as their potential for long term damage has yet to be determined.

The significance of EU topics in national media. Has there been an Europeanization of reporting in the national media? Bruges Political Research Papers No. 27/November 2012

Criticisms are often voiced at the fact that there is no well-informed European public. However, as the process of European integration has advanced, the media have been devoting more resources and space to the coverage of European affairs. At the same time, the national media have gone from being mere transmitters of information to having their own voice on European issues. In this respect, the media have emerged as actors capable of influencing the opinions of citizens, thereby contributing to the emergence of a European public sphere. The present study analyzes whether a Europeanization of the national media has taken place by studying how national newspapers provide information in Europe and whether a European public sphere is emerging. The results reveal that some European topics have experienced a certain Europeanization, but there is still an absence of European debate in the respective national public spheres.

Towards Better Use of Credit Reporting in Europe. CEPS-ECRI Task Force Report, September 2013

This report discusses how the current EU credit reporting systems meet the demands of the different stakeholders in the credit granting and management process, and what is needed to improve these systems. As credit reporting is a tool for responsible lending and for ensuring financial inclusion of consumers, it argues that the needs of EU credit markets and consumers should be the basis for assessing the current regulation and its functionality. How a creditor assesses the risk and the creditworthiness of a customer is at the core of successful and safe crediting. Facilitating this assessment process, within the boundaries of data protection laws, is a key building block for making well-informed credit decisions.