The consent problem within DNA biobanks

Large prospective biobanks are being established containing DNA, lifestyle and health information in order to study the relationship between diseases, genes and environment. Informed consent is a central component of research ethics protection. Disclosure of information about the research is an essential element of seeking informed consent. Within biobanks, it is not possible at recruitment to describe in detail the information that will subsequently be collected because people will not know which disease they will develop. It will also be difficult to describe the specific research that will be performed using the biobank, other than to stipulate categories of research or diseases that are not included. Potential subjects can only be given information about the sorts of research that will be performed and by whom. Organisations responsible for biobanks usually argue that this disclosure of information is adequate when seeking informed consent, especially if coupled with a right to withdraw, as it would not be feasible or it would be too expensive to seek consent renewal on a regular basis. However, there are concerns about this 'blanket consent' approach'. Consent waivers have also been proposed in which research subjects entrust their consent with an independent third party to decide whether subsequent research using the biobank is consistent with the original consent provided by the subject.     

Psychoneuroimmunology: The problem of the situatedness of illness and the conceptualization of healing

Psychoneuroimmunology claims to go beyond narrow biological perspectives of illness to consider behavioral components as an integral part of health and disease. The conceptualization of the embodiment of behavioral dimensions and how they may be represented in terms of interaction between the central nervous system and the immune system are therefore central theoretical issues. Psychoneuroimmunology is thus an arena in which questions about the body and person in context should come to the fore. There are multiple approaches in the psychoneuroimmunological literature, including those which attempt to address in some fashion the issue of the situatedness of illness. It is argued here that the problem of the representation of situatedness is the primary axis of tension in current research and writing in psychoneuroimmunology. Diverse attempts to represent extremely complex (and non-linear) relationships between behavioral and biological dimensions of immune system functioning drive a number of researchers, though they operate under disciplinary, institutional, and funding constraints in the U.S. which tend to work against the development of competing or radical models within psychoneuroimmunology itself.     

The size distribution of protein families within different types of folds

It is well known that the structure is currently available only for a small fraction of known protein sequences. It is urgent to discover the important features of known protein sequences based on present protein structures. Here, we report a study on the size distribution of protein families within different types of folds. The fold of a protein means the global arrangement of its main secondary structures, both in terms of their relative orientations and their topological connections, which specify a certain biochemical and biophysical aspect. We first search protein families in the structural database SCOP against the sequence-based database Pfam, and acquire a pool of corresponding Pfam families whose structures can be deemed as known. This pool of Pfam families is called the sample space for short. Then the size distributions of protein families involving the sample space, the Pfam database and the SCOP database are obtained. The results indicate that the size distributions of protein families under different kinds of folds abide by similar power-law. Specially, the largest families scatter evenly in different kinds of folds. This may help better understand the relationship of protein sequence, structure and function. We also show that the total of proteins with known structures can be considered a random sample from the whole space of protein sequences, which is an essential but unsettled assumption for related predictions, such as, estimating the number of protein folds in nature. Finally we conclude that about 2957 folds are needed to cover the total Pfam families by a simple method.     

From Indians to Chicanos: The Dynamics of Mexican-American Culture

From Indians to Chicanos: The Dynamics of Mexican- American Culture. Second Edition. James Diego Vigil. Prospect Heights, IL: Waveland Press, 1998. 324 pp.     

From Indians to Chicanos: The Dynamics of Mexican-American Culture

From Indians to Chicanos: The Dynamics of Mexican-American Culture. 2nd edition. James Diego Vigil. Prospect Heights, IL: Waveland Press, 1998. 324 pp.     

Genetic determination of mental activity parameters in the families of schizophrenic patients

Psychological parameters of mental activity (30 in total) and their genetic determination were studied in 67 families of schizophrenia patients (67 patients, 107 parent, and 30 sibs). Abnormalities of most of the examined characteristics were found in both the patients and their healthy relatives. Parameters of attention shifting and emotionality exhibited the largest genetic component (25-75 and 17-98%, respectively) in all analyzed groups of relatives (probands-affected sibs, probands-healthy sibs, healthy parents-healthy children, affected parents-affected children). Significant impact of genetic factors was also found in parameters "steadiness of attention under conditions of continuous concentration," "mediated retention span" "productivity of arbitrary retention by reproduction data," "personal anxiety level," "reflection of unusual social groups," and "self-assessment." The relationships among the characteristics examined in the system of mental activity were established by means of cluster analysis. The results of this study can be used in medical genetic counseling for identifying persons at high risk for schizophrenia.     

The interpretations of fox possession: Illness as metaphor

Although fox possession is a rare phenomenon in contemporary Japan, it is a matter of concern in psychiatry and in folk healing. The case study presented here deals with the social process of role transformation, from client to shaman, as a way of self healing. The discussion then assumes that fox possession renders multiple interpretations and argues that it is, in fact, a metaphorical representation in much the same way that biomedical interpretation is. The argument also proposes that an etiological (causal) understanding of fox possession is less productive than a metaphorical one.     

Prevalence of Helicobacter pylori CagA-producing strains within families

During prophylactic examination of blood sera taken from the members of 59 families by the enzyme immunoassay, antibodies to H. pylori and CagA protein were determined. As shown in this study, the children of non-infected mothers proved to be infected in 6.3% of cases and the children of infected mothers, in 72.1% of cases (p < 0.001). The children of non-infected fathers were H. pylori-positive in 71.4% and those of infected fathers, in 58.4% of cases. The CagA status was found to coincide in mothers and their children (p = 0.01), but not in fathers and their children. These data indicate that children acquire H. pylori infection from the members of their family, mainly from their mothers.     

Computational analysis of ligand relationships within target families

Computational tools for the large-scale analysis and prediction of ligand-target interactions and the identification of small molecules having different selectivity profiles within target protein families complement research in chemical genetics and chemogenomics. For computational analysis and design, such tasks require a departure from the traditional focus on single targets, hit identification, and lead optimization. Recently, studies have been reported that profile compounds in silico against arrays of targets or systematically map ligand-target space. In order to identify small molecular probes that are suitable for chemical genetics applications, molecular diversity needs to be viewed in a way that partly differs from principles guiding conventional library design.     

Phylogenetic relationships within cation transporter families of Arabidopsis

Uptake and translocation of cationic nutrients play essential roles in physiological processes including plant growth, nutrition, signal transduction, and development. Approximately 5% of the Arabidopsis genome appears to encode membrane transport proteins. These proteins are classified in 46 unique families containing approximately 880 members. In addition, several hundred putative transporters have not yet been assigned to families. In this paper, we have analyzed the phylogenetic relationships of over 150 cation transport proteins. This analysis has focused on cation transporter gene families for which initial characterizations have been achieved for individual members, including potassium transporters and channels, sodium transporters, calcium antiporters, cyclic nucleotide-gated channels, cation diffusion facilitator proteins, natural resistance-associated macrophage proteins (NRAMP), and Zn-regulated transporter Fe-regulated transporter-like proteins. Phylogenetic trees of each family define the evolutionary relationships of the members to each other. These families contain numerous members, indicating diverse functions in vivo. Closely related isoforms and separate subfamilies exist within many of these gene families, indicating possible redundancies and specialized functions. To facilitate their further study, the PlantsT database (http://plantst.sdsc.edu) has been created that includes alignments of the analyzed cation transporters and their chromosomal locations.     

Variability within families and the evolution of body-condition-dependent dispersal

In a population where body condition varies between and within families, we investigate the evolution of dispersal as a function of body condition ('strength', e.g. body size). Strong individuals are better competitors in a weighted lottery. If body condition does not influence survival during dispersal, then there is no unique evolutionarily stable strategy. Instead, there are infinitely many dispersal strategies that all lead to the same non-dispersing weight in a patch. These strategies are all selectively neutral but determine wildly different relationships between body condition and disposal probability. This may explain why there is no consistent pattern between body condition and dispersal found in empirical studies. If body condition influences survival during dispersal, then neutrality is removed and individuals with higher survival probability disperse. Dispersal may be the competitively weaker individuals if smaller body size helps to avoid dispersal risks.     

Conservation of electrostatic properties within enzyme families and superfamilies

Electrostatic interactions play a key role in enzyme catalytic function. At long range, electrostatics steer the incoming ligand/substrate to the active site, and at short distances, electrostatics provide the specific local interactions for catalysis. In cases in which electrostatics determine enzyme function, orthologs should share the electrostatic properties to maintain function. Often, electrostatic potential maps are employed to depict how conserved surface electrostatics preserve function. We expand on previous efforts to explain conservation of function, using novel electrostatic sequence and structure analyses of four enzyme families and one enzyme superfamily. We show that the spatial charge distribution is conserved within each family and superfamily. Conversely, phylogenetic analysis of key electrostatic residues provide the evolutionary origins of functionality.     

The threshold bootstrap clustering: a new approach to find families or transmission clusters within molecular quasispecies

Background

Phylogenetic methods produce hierarchies of molecular species, inferring knowledge about taxonomy and evolution. However, there is not yet a consensus methodology that provides a crisp partition of taxa, desirable when considering the problem of intra/inter-patient quasispecies classification or infection transmission event identification. We introduce the threshold bootstrap clustering (TBC), a new methodology for partitioning molecular sequences, that does not require a phylogenetic tree estimation.

Methodology/Principal Findings

The TBC is an incremental partition algorithm, inspired by the stochastic Chinese restaurant process, and takes advantage of resampling techniques and models of sequence evolution. TBC uses as input a multiple alignment of molecular sequences and its output is a crisp partition of the taxa into an automatically determined number of clusters. By varying initial conditions, the algorithm can produce different partitions. We describe a procedure that selects a prime partition among a set of candidate ones and calculates a measure of cluster reliability. TBC was successfully tested for the identification of type-1 human immunodeficiency and hepatitis C virus subtypes, and compared with previously established methodologies. It was also evaluated in the problem of HIV-1 intra-patient quasispecies clustering, and for transmission cluster identification, using a set of sequences from patients with known transmission event histories.

Conclusion

TBC has been shown to be effective for the subtyping of HIV and HCV, and for identifying intra-patient quasispecies. To some extent, the algorithm was able also to infer clusters corresponding to events of infection transmission. The computational complexity of TBC is quadratic in the number of taxa, lower than other established methods; in addition, TBC has been enhanced with a measure of cluster reliability. The TBC can be useful to characterise molecular quasipecies in a broad context.     

Ataques de nervios in the Puerto Rican diagnostic interview schedule: The impact of cultural categories on psychiatric epidemiology

This paper examines the effect of the cultural category ataques de nervios on responses to the Puerto Rican Diagnostic Interview Schedule (DIS), a Spanish version of structured psychiatric diagnostic interview developed for the NIHM Epidemiologic Catchment Area study. An ataque de nervios scale was created from the Somatization items of the DIS to explore the effect of this culturally meaningful category of distress on responses to a standard psychiatric interview. Analysis of 1,513 cases from a representative sample of the island of Puerto Rico indicated that people reporting ataque symptoms fit the social characteristics described for ataques sufferers in the ethnographic literature. Qualitative data indicated that Puerto Ricans were reporting ataques de nervios in the panic section of the DIS. Questions are raised about the validity of the somatization and panic sections of the DIS in cross-cultural research with Hispanics.     

On the phylogeny of families and genera within the Temnocephalida

Temnocephalida includes species demonstrating many intermediate steps presenting the transition from commensalism to parasitism. Dramatic morphological changes also occurred within this group but the number of supraspecific taxa is small, making the Temnocephalida an excellent model for evolutionary studies. Having summarised original and relevant published morphological data, we suggest a cladogram (phylogenetic tree) which nearly fully resolves the order of branching of families and main genera within the Temnocephalida. We also introduce a new family, the Diceratocephalidae nov. fam. This revised version was published online in July 2006 with corrections to the Cover Date.