Data resolution: a jackknife procedure for determining the consistency of molecular marker datasets

The results of genetic diversity studies using molecular markers not only depend on the biology of the studied objects but also on the quality of the marker data. Poor data quality may hamper the correct answering of biological questions. A new statistic is proposed to estimate the quality of a marker data set with regard to its ability to describe the structure of the biological material under study. This statistic is called data resolution (DR). It is calculated by splitting a marker data set at random into two sets each with half the number of markers. In each set, similarities between all pairs of objects are calculated. Subsequently, the similarities obtained for the two sets are correlated. This process is repeated a large number of times. The average of the correlation coefficients obtained in this way is the DR of the dataset. In the present paper, the DR statistic is applied to four studies involving amplified fragment length polymorphism as well as micro-satellite markers. In addition, some properties and possible applications of DR are discussed, including the prediction of the added value of scoring additional markers, and the determination of which similarity measure is, apart from genetical considerations, most appropriate for analyzing the data.     

A genetical model for emergenesis: in memory of Laurence H. Snyder, 1901-86.

When a phenotype is determined by a specific gene combination of several loci, it is called an emergenic trait. Such a trait, although genetically controlled, does not usually run in families, since the specific gene combination can hardly be preserved in the process of reproduction. The present paper suggests a concrete genetical model to account for the phenomenon that there is little resemblance between siblings and parent-child pairs with respect to this trait. The genetical model is multiple homozygosis for all loci involved in the gene configuration. The properties of such a trait in a random mating population for all families, as well as for the segregating families only, are investigated. Some of the difficulties in estimating the genetical parameters on the basis of empirical data are also discussed.     

Gene regulatory network reconstruction using Bayesian networks, the Dantzig Selector, the Lasso and their meta-analysis

Modern technologies and especially next generation sequencing facilities are giving a cheaper access to genotype and genomic data measured on the same sample at once. This creates an ideal situation for multifactorial experiments designed to infer gene regulatory networks. The fifth "Dialogue for Reverse Engineering Assessments and Methods" (DREAM5) challenges are aimed at assessing methods and associated algorithms devoted to the inference of biological networks. Challenge 3 on "Systems Genetics" proposed to infer causal gene regulatory networks from different genetical genomics data sets. We investigated a wide panel of methods ranging from Bayesian networks to penalised linear regressions to analyse such data, and proposed a simple yet very powerful meta-analysis, which combines these inference methods. We present results of the Challenge as well as more in-depth analysis of predicted networks in terms of structure and reliability. The developed meta-analysis was ranked first among the 16 teams participating in Challenge 3A. It paves the way for future extensions of our inference method and more accurate gene network estimates in the context of genetical genomics.     

Molecular Typing of MRSA and of Clinical Staphylococcus aureus Isolates from Ia?i,Romania

Romania is one of the countries with the highest prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in the world. To obtain data on affiliation of MRSA to strains and clonal complexes and on the population of methicillin susceptible S. aureus (MSSA), clinical isolates from bloodstream infections, skin and soft tissue infections as well as from screening swabs were collected at hospitals in Ia?i, a city in the North-Eastern part of Romania. Isolates were characterised by microarray hybridisation. Nearly half of all isolates (47%), and about one third (34%) of bloodstream isolates were MRSA. The prevalence of the Panton-Valentine leukocidin (PVL) was also high (31% among MRSA, 14% among MSSA). The most common MRSA strain was a PVL-negative CC1-MRSA-IV that might have emerged locally, as a related MSSA was also common. PVL-positive CC8-MRSA-IV (“USA300”) and PVL-negative ST239-like MRSA-III were also frequently found while other MRSA strains were only sporadically detected. Among MSSA, PVL-positive CC121 as well as PVL-negative CC1, CC22 and CC45 predominated. Although this study provides only a snapshot of S. aureus/MRSA epidemiology in Romania, it confirms the high burden of MRSA and PVL on Romanian healthcare settings.     

Genetical distance and dermatoglyphic characters. III. Dermatoglyphic distances within twin pairs, between left and right sides and between normals and 21-trisomics

The dermatoglyphic (genetical) distance coefficients have been estimated within monozygotic and dizygotic twin pairs, between left and right sides of the same individual and between normal subjects and 21-trisomics. All the coefficients have been based, in turn, on frequencies of fingertip, palmar and sole pattern elements, separately and for all characters combined. Quantitative variables (pattern intensities) have also been used for independent evaluation of the C2H distance coefficient in monozygotic and dizygotic twins, and in 21-trisomics as compared with normal individuals. The values of a distance have then been considered in relation to the degree of genetical likeness between the compared items as well as to the relative contribution of each pattern combination to the overall value of a distance. Some limitations in the interpretation of the results, connected mainly with statistical procedures, are also discussed.     

Population genetic studies in the Balkans. I. Serum proteins

Within a study of the genetics of Southeastern European populations seven serum protein polymorphisms (AMY2, BF, C3, CP, GC, HPA, TF) were examined in three samples of Aromuns (Albania: the village of Andon Poci, province Gjirocaster, Republic of Macedonia: Stip region, Romania: the village Kogalniceanu, province Dobruja) and four reference samples (Albanians: Tirana, Romanians: Constanta and Ploiesti as well as Greeks (Northeastern Greece)). The Aromun samples from Albania and Romania form one separate cluster and the reference samples together with the Aromuns from Macedonia (Stip region) form a second one.     

The genetical analysis of covariance structure.

The analysis of covariance structures (J?reskog, 1973) is adapted to the simultaneous maximum likelihood estimation of genetical and environmental factor loadings and specific variances. The goodness of fit is tested by chi square and standard errors of parameter estimates can be obtained. Any linear model used in univariate genetical analyses can be extended to the multivariate case. Most biological hypotheses about the relationships between variables can be specified by a variety of factor models. Individual parameters can be given fixed values or set to zero and hypotheses concerning the congruence of genetical and environmental correlations can be tested. The method is illustrated with published twin data on cognitive abilities.     

Seroprevalence of Neospora caninum infection on dairy cattle in farms from southern Romania

Neospora caninum, a coccidian parasite closely related to Toxoplasma gondii, is one of the major causes of abortion in cattle worldwide. Conventional serological techniques, such as the indirect fluorescent antibody test and enzyme-linked immunosorbent assay (ELISA), are routinely used in adult animals and aborted fetuses for the detection of anti- N. caninum antibodies. In Romania, infection with N. caninum in cattle has been reported recently, but only in limited areas from the north and central parts of the country. Therefore, the aim of this study was to obtain additional seroepidemiological data on infection with N. caninum on dairy farms from the south of Romania. A total of 258 blood samples was analyzed from 230 dairy cows and 28 calves from 9 dairy farms in southern Romania; the presence of specific IgG antibodies against N. caninum was determined using an indirect ELISA test. The average seroprevalence was 40.3%, but the within-herd prevalence ranged between 11.5 and 80.0%; the seroprevalence in dairy cows was 41.7%, while in calves it was 28.6%. Of the positive samples, 74.0% (77/104) had a high positive reaction (S/P ratio more than 1.0), while 26.0% (27/104) had a low positive reaction (S/P ratio between 0.5 and 1.0). This study indicates that N. caninum infection is widespread in the south of Romania, which could explain the causes of abortions registered in some herds in the studied area. However, a serological screening across the country is planned in order to assess the actual national prevalence of N. caninum infection, followed by implementation of a prevention and control program.     

A study of the A-1A-2BO blood group system and ABO(H) secretion in six endogamous groups of Punjab

2,596 Aroras and 2,629 Khatris comprising six endogamous groups of the Punjabis have been studied for A₁A₂BO blood groups and secretion of ABO(H) group specific substances. The values of chi-square and the genetical difference (G²) among these groups do not show statistically significant differences in these groups regarding the genetical characters studied. There is a closer affinity between Beri and Bunjahi on the one hand and Uttaradhi and Dhakhandian on the other and also between Uttaradhi and Khukhran; Dhakhandian and Sareen show a great difference among themselves as well as with other groups. The comparison of ABO blood group distribution and secretor factor among the different populations of India show that the distribution is similar among the North Indians.     

Learning Gene Networks under SNP Perturbations Using eQTL Datasets

The standard approach for identifying gene networks is based on experimental perturbations of gene regulatory systems such as gene knock-out experiments, followed by a genome-wide profiling of differential gene expressions. However, this approach is significantly limited in that it is not possible to perturb more than one or two genes simultaneously to discover complex gene interactions or to distinguish between direct and indirect downstream regulations of the differentially-expressed genes. As an alternative, genetical genomics study has been proposed to treat naturally-occurring genetic variants as potential perturbants of gene regulatory system and to recover gene networks via analysis of population gene-expression and genotype data. Despite many advantages of genetical genomics data analysis, the computational challenge that the effects of multifactorial genetic perturbations should be decoded simultaneously from data has prevented a widespread application of genetical genomics analysis. In this article, we propose a statistical framework for learning gene networks that overcomes the limitations of experimental perturbation methods and addresses the challenges of genetical genomics analysis. We introduce a new statistical model, called a sparse conditional Gaussian graphical model, and describe an efficient learning algorithm that simultaneously decodes the perturbations of gene regulatory system by a large number of SNPs to identify a gene network along with expression quantitative trait loci (eQTLs) that perturb this network. While our statistical model captures direct genetic perturbations of gene network, by performing inference on the probabilistic graphical model, we obtain detailed characterizations of how the direct SNP perturbation effects propagate through the gene network to perturb other genes indirectly. We demonstrate our statistical method using HapMap-simulated and yeast eQTL datasets. In particular, the yeast gene network identified computationally by our method under SNP perturbations is well supported by the results from experimental perturbation studies related to DNA replication stress response.     

Ex situ conservation of plant diversity in Romania: A synthesis of threatened and endemic taxa

Romania hosts a relatively high species diversity, including 3,829 vascular and 979 non-vascular spontaneous plant taxa. Multiple national red lists exist, with the number of taxa assessed as threatened varying greatly between them, from 548 to 1,438, and with number of taxa assigned to a given threat category also varying between the different sources. A composite list including all taxa mentioned in at least one of the selected red listings from Romania is required in order to compensate for this lack of consensus and to assess their ex situ conservation status. In this study, we synthesized data from the national red lists and counted 1,220 spontaneous vascular plant species and 201 subspecies, of which 77 are endemic and 76 subendemic for Romania. In addition, 18 non-red-listed endemics and 14 subendemics have been added, bringing the total to 1,453 threatened and (sub)endemic plant taxa, representing almost 38% of the total native vascular flora of Romania. Despite the large network of protected areas in Romania, many taxa are still being threatened with extinction in the region mainly due to anthropogenic pressure. Several ex situ conservation measures have been employed to assure a more substantial buffer against plant extinction in the wild, supported by thorough and adequate conservation strategies and multiple means to reintroduce taxa back to their natural habitats. Consequently, our second aim was to evaluate the ex situ conservation status of these threatened and (sub)endemic plants from Romania, focussing on both conventional methods (cultivation in botanic gardens, seed banking) and biotechnological approaches (in vitro tissue culture, medium-term storage and cryostorage). Of the 1,453 taxa included in our list, 642 (44.2%) are conserved by ex situ approaches. Of these, 524 are harboured in the most important botanic gardens throughout Romania, while 156 are currently held in long-term seed banks locally or in the Millennium Seed Bank of the Royal Botanic Garden, Kew (UK). Conversely, only 64 taxa from the list are preserved at the national level through in vitro cultures, and cryopreservation protocols have been developed for only 8 taxa. Overall, more than half of the threatened and (sub)endemic vascular flora from Romania remains unprotected outside the classical in situ conservation measures. For red-listed bryophytes, only 0.6% are preserved in national ex situ collections. Moreover, some aspects related to population genetic studies and the genetic stability of ex situ conserved plants are also briefly discussed, as essential prerequisites for applied biodiversity conservation programs. Finally, considering the distribution range of targeted taxa, we included a synthesis of biotechnological approaches at both national and international level. Our study presents not only a first assessment of the ex situ conservation status of national red listed flora, but also, to our knowledge, the most comprehensive and updated overview of the rare, threatened and (sub)endemic taxa from Romania. This evaluation will provide a supporting tool for national decision- and policy-making actions for biodiversity conservation, using both in situ and ex situ approaches. We also highlight the need for an updated red list for the Romanian flora that accurately follows the IUCN assessment criteria and protocols.     

Population genetical study of natural hybridization betweenPapio anubis andP. hamadryas

The natural hybridization betweenPapio anubis andP. hamadryas in central Ethiopia was studied from a population genetical perspective. Studies were made using electrophoretical blood protein variations as markers in order to clarify the genetic relationship between them. A total of 563 samples from ten populations which were collected in the field studies with a socioecologist in 1976 and 1979 were examined for 34 blood protein loci. Ten of the 34 loci showed polymorphism. The Tf, PA-2 and Es were found to be effective for discriminating between the anubis and hamadryas. Genetic variability, hybridization rate, genetic distance, migration rates and correlations between genetical and morphological and between genetical and behavioral indices were computed and analyzed. The results of the present genetic survey revealed that most of the populations from which the author collected blood samples were more or less hybridized. The Nei's (1975) genetic distance between the two species was estimated to be 0.0679 at most. As this value is too small to consider these species as real biological species, it is supposed that the natural hybrid zone is fairly wide and still expanding now. This work was supported in part by Grants in aid for scientific research (Overseas scientific research, 1975) and of the Overseas Special Research Programme of the Primate Research Institute, Kyoto University in 1978 by Ministry of Education, Science and Culture.     

Genetic studies on reference strains of mutans streptococci

Twenty four reference strains (serotype a-h) belonging to the mutans group of streptococci were compared for DNA fragment patterns of rDNA after treatment with Hind III. It was shown that Streptococcus cricetus (serotype a), S. rattus (serotype b), and S. downei (serotype h) reveals comparatively homogeneous patterns while S. mutans (serotype c, e and f) exhibits differences between the different serotypes as well as within single serotypes. S. sobrinus had an intermediary diversity. These data support the previous findings that S. mutans is heterogeneous at the serological, biochemical and genetical level.     

Metapopulation dynamics in a regional population of the blue-winged grasshopper (Oedipoda caerulescens; Linnaeus, 1758)

For two consecutive years we registered the presence (or absence) of blue winged grasshoppers (Oedipoda caerulescens; Linnaeus, 1758) on 312 habitat patches of differing size in a region of more than 3000 ha. The data show that presence of grasshoppers on a habitat patch is dependent on patch size as well as on patch isolation. We used an ecological incidence model to describe the metapopulation dynamics of the regional population and derived the parameters for this model from presence-absence data and observations of Oedipoda dispersion. The analysis shows that local extinction of grasshopper populations is influenced by strong fluctuations of environmental conditions and that for a number of small patches in our region recolonization is important for the presence of O. caerulescens. Colonization probability, as derived using the incidence model, is in good agreement with estimates from a population genetical analysis.     

Badenian and Sarmatian s.str. from the Carpathian area: Taxonomical notes concerning the Hungarian and Romanian small vertebrates and report on the ruminants from the Felsőtárkány Basin

Over the last decade, important progress has been made in the study of the mammal successions from Hungary and Romania. A critical review of the taxonomy of the published small mammals is provided herein, as well as some new data and an overview of the accompanying vertebrate fauna (excluding fishes) in their stratigraphic context. In addition, the first data regarding the ruminants from Mátrasz?l?s and Fels?tárkány are presented. This contribution aims to characterize the middle to earliest late Miocene fossil record from these countries, and provide important data for the chrono(bio)stratigraphic and palaeoenvironmental studies at the European scale.     

Evolutionary trends in Albanian anthropological materials

The documentation of the brachy-cephalization, as long-term process of transformation, is based on studies of human skeletal remains from different times as well as on the available metric data of the recent population samples. Apart from a range of diachronic sequences, the author tries to determined the beginning and speed of the process according to the present state of knowledge: additionally he looks for correlated ethnohistorical events. To confirm the general opinion, the genetical background and the probable involvement of some external factors are discussed this article.     

MtDNA polymorphism in the Hungarians: comparison to three other Finno-Ugric-speaking populations

Mitochondrial DNA sequence variation as well as restriction site polymorphisms were examined in 437 individuals from four Finno-Ugric-speaking populations. These included the Hungarians (Budapest region and the Csángós from Hungary and Romania), the Finns and two Saami groups from northeastern Finland (Inari Saami and Skolt Saami), and the Erzas from central Russia. The mtDNA data obtained in this study were combined with our previous data on Y chromosomal variation for eight different loci in these populations. The genetic variation observed among the Hungarians resembled closely that found in other European populations. The Hungarians could not be distinguished from the neighboring populations (e.g., the Austrians) any more than from their Finno-Ugric linguistic relatives.     

Genetical Genomics of Behavior: A Novel Chicken Genomic Model for Anxiety Behavior

The identification of genetic variants responsible for behavioral variation is an enduring goal in biology, with wide-scale ramifications, ranging from medical research to evolutionary theory on personality syndromes. Here, we use for the first time a large-scale genetical genomics analysis in the brains of chickens to identify genes affecting anxiety as measured by an open field test. We combine quantitative trait locus (QTL) analysis in 572 individuals and expression QTL (eQTL) analysis in 129 individuals from an advanced intercross between domestic chickens and Red Junglefowl. We identify 10 putative quantitative trait genes affecting anxiety behavior. These genes were tested for an association in the mouse Heterogeneous Stock anxiety (open field) data set and human GWAS data sets for bipolar disorder, major depressive disorder, and schizophrenia. Although comparisons between species are complex, associations were observed for four of the candidate genes in mice and three of the candidate genes in humans. Using a multimodel approach we have therefore identified a number of putative quantitative trait genes affecting anxiety behavior, principally in chickens but also with some potentially translational effects as well. This study demonstrates that chickens are an excellent model organism for the genetic dissection of behavior.