Microbiomes in bioenergy production: From analysis to management

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Personality endophenotypes for bipolar affective disorder: a family-based genetic association analysis

Genetic analyses of complex conditions such as bipolar disorder (BD) may be facilitated by the use of intermediate phenotypes. Various personality traits are overrepresented in people with BD and their unaffected relatives, and may constitute genetically transmitted risk factors or endophenotypes of the illness. In this study, we administered a battery of seven different personality questionnaires comprising 19 subscales to 31 Caucasian BD families (n = 241). Ten of these personality traits showed significant evidence of heritability and were therefore selected as candidate endophenotypes. In addition, a principal components analysis produced two heritable components (negative affect and appetitive drive), which accounted for a considerable proportion of the variance (29% + 12%) and were also used in the analysis. A family-based quantitative association study was carried out using the orthogonal model from the quantitative transmission disequilibrium tests (QTDT) program. Monte Carlo permutations (M = 500), which allow for non-normal data and provide a global P value, corrected for multiple testing, were used to calculate empirical P values for the within-family component of association. The 3' untranslated region repeat polymorphism of the dopamine transporter gene (SLC6A3) was associated with self-directedness (P < 0.0001) and negative affect (P = 0.010). The short allele of the serotonin transporter gene (SLC6A4) promoter polymorphism showed a trend toward association with higher harm avoidance (P = 0.016) and negative affect (P = 0.028). The catechol-o-methyltransferase val158met polymorphism was weakly associated with the personality traits, 'Spirituality' (P = 0.040) and irritable temperament (P = 0.022). Furthermore, the met allele of the brain-derived neurotrophic factor val66met polymorphism was associated with higher hyperthymic temperament scores. We raise the possibility that the 10R allele of the SLC6A3 repeat polymorphism and the short allele of the SLC6A4 promoter variant constitute risk factors for irritable-aggressive and anxious-dysthymic subtypes of BD, respectively.     

r-selected reproductive strategies among Hungarian Gipsies: A preliminary analysis

The Gipsies, a particular ethnic and social group living mostly in the Eastern European countries, have been studied in terms of r- and K-selection. Considering the variables of fertility, birth spacing, mortality, age distribution, and physical parameters, they proved to be more r-selected than the Hungarians. The main factors bringing about these differences on the scale of r- and K-strategy come from both genetic and cultural biases. Resource unpredictability and social uncertainty, important components of the Gipsies' way of life, contribute to their higher fertility and mortality. Other characteristics, such as a female surplus in the birth sex ratio and the good survival capacity of the “premature” Gipsy infants, seem to show genetic influences as “racial” traits. Finally, a particular family arrangement characteristic of Gipsies, the father-absent household, is likely to have influence on their early sexual activity, even promiscuity, and unstable pair bonds. These analyses, that should be completed with further detailed investigations of social factors, may contribute to the understanding and improvement of the Gipsies' living conditions, after their ignorance in the Communist regime.     

Genetic studies in a Hungarian isolate: Ivád

A total of 675 individuals from the Hungarian isolate Ivád has been typed for 25 genetic polymorphisms. This sample was devided into three subgroups: 1. Full Ivádys (both spouses and their ancestors are members of the Ivád family; n = 330), 2. Half Ivádys (= either husband or wife and his or her, respectively, ancestors are from the Ivády family, the other partner from the outside population; n = 267), and 3. Non-Ivádys (married couples not belonging to the Ivády family; n = 78). The main concern of this paper is 1. to show to intra-Ivád variability of the distribution of various genetic parameters (allele frequencies, heterozygosity, gene diversity etc.) among these three groups, and 2. to analyze the impact of the different mating patterns of these groups on the genetic structure of the Ivád population. From the comparison of the Ivád gene frequencies with that of neighbouring populations (Pétervására and Erd?k?vesd) it is seen that drift or founder effects played some role. Within the Ivád population only few gene frequencies show a marked heterogeneity. As expected the average heterozygosity in Full Ivádys is somewhat lower than in Half Ivádys and Non-Ivádys, respectively. The pattern of genetic relationships of the various Ivád groups is in conformity with the demographic and historical facts of this village.     

Molecular analysis of cystic fibrosis in the Hungarian population

Summary Hungarian cystic fibrosis (CF) families (n = 33) including 114 family members have been analysed for the presence of the F508 mutation within the cystic fibrosis transmembrane conductance regulator (CFTR) gene, and have been haplotyped with probes for restriction fragment length polymorphisms (RFLPs) known to be linked to the CFTR gene. The F508 deletion was present in 64% of CF chromosomes. As in many other populations, linkage disequilibrium was found between the CF locus and the haplotype B (XV-2c: allele 1, KM1-9: allele 2), which accounts for 95% of F508 CF chromosomes in our families.     

CLAGen: a tool for clustering and annotating gene sequences using a suffix tree algorithm

Most multiple gene sequence alignment methods rely on conventions regarding the score of a multiple alignment in pairwise fashion. Therefore, as the number of sequences increases, the runtime of sequencing expands exponentially. In order to solve the problem, this paper presents a multiple sequence alignment method using a linear-time suffix tree algorithm to cluster similar sequences at one time without pairwise alignment. After searching for common subsequences, cross-matching common subsequences were generated, and sometimes inexact matching was found. So, a procedure aimed at masking the inexact cross-matching pairs was suggested here. In addition, BLAST was combined with a clustering tool in order to annotate the clusters generated by suffix tree clustering. The proposed method for clustering and annotating genes consists of the following steps: (1) construction of a suffix tree; (2) searching and overlapping common subsequences; (3) grouping subsequence pairs; (4) masking cross-matching pairs; (5) clustering gene sequences; (6) annotating gene clusters by the BLAST search. The performance of the proposed system, CLAGen, was successfully evaluated with 42 gene sequences in a TCA cycle (a citrate cycle) of bacteria. The system generated 11 clusters and found the longest subsequences of each cluster, which are biologically significant.     

From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis

This paper proposes a new method to reverse engineer gene regulatory networks from experimental data. The modeling framework used is time-discrete deterministic dynamical systems, with a finite set of states for each of the variables. The simplest examples of such models are Boolean networks, in which variables have only two possible states. The use of a larger number of possible states allows a finer discretization of experimental data and more than one possible mode of action for the variables, depending on threshold values. Furthermore, with a suitable choice of state set, one can employ powerful tools from computational algebra, that underlie the reverse-engineering algorithm, avoiding costly enumeration strategies. To perform well, the algorithm requires wildtype together with perturbation time courses. This makes it suitable for small to meso-scale networks rather than networks on a genome-wide scale. An analysis of the complexity of the algorithm is performed. The algorithm is validated on a recently published Boolean network model of segment polarity development in Drosophila melanogaster.     

Urine as a source for clinical proteome analysis: From discovery to clinical application

The success of clinical proteome analysis should be assessed based on the clinical impact following implementation of findings. Although there have been several technological advancements in mass spectrometry in the last years, these have not resulted in similar advancements in clinical proteomics. In addition, application of proteomic biomarkers in clinical diagnostics and practical improvement in the disease management is extremely rare. In this review, we discuss the relevant issues associated with identification of robust biomarkers of clinical value. Urine appears to be an ideal source of biomarkers, for theoretical, methodological, and practical reasons. Therefore, this review is focused on the search for biomarkers in urine within the last decade. Urine can be used for non-invasive assessment of a variety of diseases including those affecting the urogenital tract and also other pathologies such as cardiovascular disease or appendicitis. We also discuss the importance of data validation, an essential step in translating biomarkers into the clinical practice. Furthermore, we examine several examples of apparently successful proteomic biomarker discovery studies and their implications for disease diagnosis, prognosis, and therapy evaluation. We also discuss some current challenges in this field and reflect on future research prospects. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.     

Comparative analysis of dermatoglyphic traits in Hungarian and Gypsy populations

We examined dermatoglyphic prints of children in 11 Hungarian and 5 Gypsy population samples (collected from 1,998 children). We compared Hungarian and Gypsy populations based on 22 finger and 24 palmar traits. In univariate comparisons the two ethnic groups differed significantly in half of the studied variables (9 finger and 14 palmar traits). We used several types of multivariate analyses of the studied traits to separate the population samples. Homogeneity analysis and discriminant analysis proved to be the most appropriate method to distinguish the populations, whereas a principal components analysis was less adequate. Multivariate analyses were conducted separately for both finger and palmar traits. Although the differences between the populations were more pronounced for palmar traits, in our study Hungarian and Gypsy populations showed the best separation when finger and palmar traits were combined for analysis, except in the principal components analysis. As expected, the Hungarian and Gypsy populations separated definitely in most statistical analyses; the main reason for this is the different origins of the two ethnic groups. The existence of the difference also shows that admixture between Hungarians and Gypsies has been small despite their living beside one another for several centuries.     

From simple to complex oscillatory behaviour: analysis of bursting in a multiply regulated biochemical system

We analyze the transition from simple to complex oscillatory behaviour in a three-variable biochemical system that consists of the coupling in series of two autocatalytic enzyme reactions. Complex periodic behaviour occurs in the form of bursting in which clusters of spikes are separated by phases of relative quiescence. The generation of such temporal patterns is investigated by a series of complementary approaches. The dynamics of the system is first cast into two different time-scales, and one of the variables is taken as a slowly-varying parameter influencing the behaviour of the two remaining variables. This analysis shows how complex oscillations develop from simple periodic behaviour and accounts for the existence of various modes of bursting as well as for the dependence of the number of spikes per period on key parameters of the model. We further reduce the number of variables by analyzing bursting by means of one-dimensional return maps obtained from the time evolution of the three-dimensional system. The analysis of a related piecewise linear map allows for a detailed understanding of the complex sequence leading from a bursting pattern with p spikes to a pattern with p + 1 spikes per period. We show that this transition possesses properties of self-similarity associated with the occurrence of more and more complex patterns of bursting. In addition to bursting, period-doubling bifurcations leading to chaos are observed, as in the differential system, when the piecewise-linear map becomes nonlinear.     

From subgenome analysis to protein structure

Groups of related genes abound in large eukaryotic genomes. In such 'subgenomes', homology modeling carried out for a few genes will probably have relevance to the entire group. Subgenomes also afford unique ways of determining protein structural information. In addition to analyses based on the quantification of residue variability in paralogs, two-way comparisons, both within and among species, help to disclose functional amino acids. Comparative studies of gene families throughout the mammalian genome will also help elucidate the functional significance of single nucleotide polymorphisms in coding regions.     

From bone biology to bone analysis

Bone development is one of the key processes characterizing childhood and adolescence. Understanding this process is not only important for physicians treating pediatric bone disorders, but also for clinicians and researchers dealing with postmenopausal and senile osteoporosis. Bone densitometry has great potential to enhance our understanding of bone development. The usefulness of densitometry in children and adolescents would be increased if the physiological mechanisms and structural features of bone were given more consideration in the design and interpretation of densitometric studies. This review gives an overview on the most relevant techniques of quantitative noninvasive bone analysis. Furthermore it describes the relationship between bone biology, selected surrogates describing the biological processes and the possibilities of measuring these surrogates specifically and precisely by the different devices. The overall recommendation for researchers in this field is to describe firstly the biological process to be analyzed (bone growth in length, remodeling or modeling, or all together), secondly the bone parameter which describes this process, and thirdly the reason for selecting a special device.     

Proteomics of breast cancer: From differential to functional analysis

From differential analysis to identify biomarkers, to functional analysis for finding new therapeutic targets, proteomics bring new comprehensive information for a better understanding of the molecular basis of oncology and new perspectives for the clinic. However the major limitation of proteomic investigations, more generally of post-genomic approaches, remains the molecular and cellular complexity of the mammary gland that is still a major challenge.