Multivariate study of lice (Insecta: Psocodea: Phthiraptera) assemblages hosted by hummingbirds (Aves: Trochilidae).

Lice were collected from 579 hummingbirds, representing 49 species, in 19 locations in Brazil, Costa Rica, Honduras, Paraguay and Peru, at elevations 0­3000 m above sea level. The following variables were included in an ecological analysis (1) host species' mean body mass, sexual size dimorphism, sexual dichromatism, migratory behaviour and dominance behaviour; (2) mean elevation, mean and predictability of temperature, mean and predictability of precipitation of the host species' geographic area; (3) prevalence and mean abundance of species of lice as measures of infestation. Ordination methods were applied to evaluate data structure. Since the traits are expressed at different scales (nominal, interval and ratio), a principal component analysis based on d-correlations for the traits and a principal coordinates analysis based on the Gower index for species were applied. Lice or louse eggs were found on 80 (13.8%) birds of 22 species. A total of 267 lice of 4 genera, Trochiloecetes, Trochiliphagus, Myrsidea and Leremenopon, were collected, with a total mean intensity of 4.6. There were positive interactions between migration behaviour and infestation indices, with elevational migrants having a higher prevalence and abundance of lice than resident birds. Further, we found weak negative correlations between host body mass and infestation indices and positive correlations between mean elevation and prevalence and abundance of Trochiliphagus. Thus, formerly unknown differences in the ecological characteristics and infestation measures of Trochiliphagus and Trochiloecetes lice were revealed, which allows a better understanding of these associations and their potential impacts on hummingbirds.

Analysis of SIRT1 Gene SNPs and Clinical Characteristics in Medication-Related Osteonecrosis of the Jaw.

Certain genetic factors, including single-nucleotide polymorphisms (SNPs) in the SIRT1 gene, have been linked to medication-related osteonecrosis of the jaw (MRONJ). This study examined four SNPs in the SIRT1 gene and implemented multivariate statistical analysis to analyze genetic and clinical factors in MRONJ patients. Genomic DNA was isolated from peripheral blood samples of 63 patients of European origin treated for MRONJ, and four SNP genotypes in the gene encoding the SIRT-1 protein were determined by Sanger sequencing. The allele frequencies measured in the MRONJ population were compared with allele frequencies measured in the European population in the National Center for Biotechnology Information Allele Frequency Aggregator (NCBI ALFA) database. Genetic and clinical factors were examined with multivariate statistical analysis. A C:A allele distribution ratio of 77.8:22.2 was measured in the rs932658 SNP. In the ALFA project, a C:A allele distribution ratio of 59.9:40.1 was detected in the European population, which was found to be a significant difference (p = 4.5 × 10-5). Multivariate statistical analysis revealed a positive correlation (0.275) between the genotype of SNP rs932658 and the number of stages improved during appropriate MRONJ therapy. It is concluded that allele A in SNP rs932658 in the SIRT1 gene acts as a protective factor in MRONJ.

Different from Trees, more than Metaphors: Branching Silhouettes-Corals, Cacti, and the Oaks.

There has long been ambiguity in the use of the term tree in phylogenetic systematics, which is a continuous source of misinterpretation of evolutionary relationships. The basic problem is that while many trees with phylogenetic or evolutionary relevance, such as cladograms, are consistent with graph theory, tree-like visualization of phylogeny may also be done via other types of graphics, especially botanical (or literal) tree drawings. As a consequence, the meaning of such diagrams is not always clear: a given picture may have multiple interpretations in its different parts and two figures that look similar may actually carry quite different information. I show that these are not merely metaphors of phylogeny and may be defined mathematically as geometric shapes called branching silhouette diagrams, the name referring to their most apparent features. They have four basic forms depending on whether the time factor is considered in their construction and the relationships portrayed are of the ancestor-descendant or sister group type. By revitalizing Darwin's early suggestions on the illustration of change in the living world, I propose the term coral for the most common forms of branching silhouette which consider time and show ancestry. The others appear rarely in present-day practice and are mostly of historical value-these are cacti (named after one of Bessey's diagrams) and two types of oaks (with reference to several of Haeckel's motifs used in depicting phylogeny in the nineteenth century). The use of these terms in phylogenetic systematics facilitates better understanding of how organization of biodiversity has been visualized in science [Bessey; cladograms; coral-thinking; Darwin; graph theory; Haeckel; phylogeny; tree thinking.].

How Fast Does Darwin's Elephant Population Grow?

In "The Origin of Species," Darwin describes a hypothetical example illustrating that large, slowly reproducing mammals such as the elephant can reach very large numbers if population growth is not affected by regulating factors. The elephant example has since been cited in various forms in a wide variety of books, ranging from educational material to encyclopedias. However, Darwin's text was changed over the six editions of the book, although some errors in the mathematics persisted throughout. In addition, full details of the problem remained hidden in his correspondence with readers of the Origin. As a result, Darwin's example is very often misinterpreted, misunderstood or presented as if it were a fact. We show that the population growth of Darwin's elephant population can be modeled by the Leslie matrix method, which we generalize here to males as well. Darwin's most often cited figure, about 19 million elephants after 750 years is not a typical outcome, actually a very unlikely result under more realistic, although still hypothetical situations. We provide a recursion formula suggesting that Darwin's original model corresponds to a tribonacci series, a proof showing that sex ratio is constant over all age classes, and a derivation of a generating function of the sequence.

Tree thinking, time and topology: comments on the interpretation of tree diagrams in evolutionary/phylogenetic systematics.

This paper presents a graph theoretical overview of tree diagrams applied extensively in systematic biology. Simple evolutionary models involving three speciation processes (splitting, budding and anagenesis) are used for evaluating the ability of different rooted trees to demonstrate temporal and ancestor-descendant relationships within or among species. On this basis, they are classified into four types: (i) diachronous trees depict evolutionary history faithfully because the order of nodes along any path agrees with the temporal sequence of respective populations or species, (ii) achronous trees show ancestor-descendant relationships for species or higher taxa such that the time aspect is disregarded, (iii) synchronous trees attempt to reveal evolutionary pathways and/or distributional patterns of apomorphic characters for organisms living at the same point of time, and (iv) asynchronous trees may do the same regardless the time of origin (e.g. when extant and extinct species are evaluated together). Trees of the last two types are cladograms, the synchronous ones emphasizing predominantly-but not exclusively-the evolutionary process within a group, while asynchronous cladograms are usually focused on pattern and infrequently on process. Historical comments and the examples demonstrate that each of these tree types is useful on its own right in evolutionary biology and systematics. In practice, separation among them is not sharp, and their features are often combined into eclectic tree forms whose interpretation is not entirely free from problems.

Components of functional diversity revisited: A new classification and its theoretical and practical implications.

Functional diversity is regarded as a key concept for understanding the link between ecosystem function and biodiversity. The different and ecologically well-defined aspects of the concept are reflected by the so-called functional components, for example, functional richness and divergence. Many authors proposed that components be distinguished according to the multivariate technique on which they rely, but more recent studies suggest that several multivariate techniques, providing different functional representations (such as dendrograms and ordinations) of the community can in fact express the same functional component. Here, we review the relevant literature and find that (1) general ecological acceptance of the field is hampered by ambiguous terminology and (2) our understanding of the role of multivariate techniques in defining components is unclear. To address these issues, we provide new definitions for the three basic functional diversity components namely functional richness, functional divergence and functional regularity. In addition, we present a classification of presence-/absence-based approaches suitable for quantifying these components. We focus exclusively on the binary case for its relative simplicity. We find illogical, as well as logical but unused combinations of components and representations; and reveal that components can be quantified almost independently from the functional representation of the community. Finally, theoretical and practical implications of the new classification are discussed.

Comparison of Boolean analysis and standard phylogenetic methods using artificially evolved and natural mt-tRNA sequences from great apes.

Boolean analysis (or BOOL-AN; Jakó et al., 2009. BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction. Mol. Phylogenet. Evol. 52, 887-97.), a recently developed method for sequence comparison uses the Iterative Canonical Form of Boolean functions. It considers sequence information in a way entirely different from standard phylogenetic methods (i.e. Maximum Parsimony, Maximum-Likelihood, Neighbor-Joining, and Bayesian analysis). The performance and reliability of Boolean analysis were tested and compared with the standard phylogenetic methods, using artificially evolved - simulated - nucleotide sequences and the 22 mitochondrial tRNA genes of the great apes. At the outset, we assumed that the phylogeny of Hominidae is generally well established, and the guide tree of artificial sequence evolution can also be used as a benchmark. These offer a possibility to compare and test the performance of different phylogenetic methods. Trees were reconstructed by each method from 2500 simulated sequences and 22 mitochondrial tRNA sequences. We also introduced a special re-sampling method for Boolean analysis on permuted sequence sites, the P-BOOL-AN procedure. Considering the reliability values (branch support values of consensus trees and Robinson-Foulds distances) we used for simulated sequence trees produced by different phylogenetic methods, BOOL-AN appeared as the most reliable method. Although the mitochondrial tRNA sequences of great apes are relatively short (59-75 bases long) and the ratio of their constant characters is about 75%, BOOL-AN, P-BOOL-AN and the Bayesian approach produced the same tree-topology as the established phylogeny, while the outcomes of Maximum Parsimony, Maximum-Likelihood and Neighbor-Joining methods were equivocal. We conclude that Boolean analysis is a promising alternative to existing methods of sequence comparison for phylogenetic reconstruction and congruence analysis.

Characterising functional strategies and trait space of freshwater macroinvertebrates.

We examined the functional strategies and the trait space of 596 European taxa of freshwater macroinvertebrates characterized by 63 fuzzy coded traits belonging to 11 trait groups. Principal component analysis was used to reduce trait dimensionality, to explain ecological strategies, and to quantify the trait space occupied by taxa. Null models were used to compare observed occupancy with theoretical models, and randomization-based analyses were performed to test whether taxonomic relatedness, a proxy of phylogenetic signal, constrains the functional trait space of freshwater macroinvertebrates. We identified four major strategies along which functional traits of the taxa examined show trade-offs. In agreement with expectations and in contrast to existing evidence we found that life cycles and aquatic strategies are important in shaping functional structure of freshwater macroinvertebrates. Our results showed that the taxonomic groups examined fill remarkably different niches in the functional trait space. We found that the functional trait space of freshwater macroinvertebrates is reduced compared to the range of possibilities that would exist if traits varied independently. The observed decrease was between 23.44 and 44.61% depending on the formulation of the null expectations. We demonstrated also that taxonomic relatedness constrains the functional trait space of macroinvertebrates.

Chronic obstructive pulmonary disease-specific gene expression signatures of alveolar macrophages as well as peripheral blood monocytes overlap and correlate with lung function.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disease characterized by progressive airflow limitation and significant extrapulmonary (systemic) effects that lead to co-morbid conditions, though the pathomechanism of COPD is largely undetermined. Alveolar macrophages (AM) derived from peripheral monocytes (MO) appear to play a key role in initiating and/or sustaining disease progression. OBJECTIVES: To identify disease- and cell type-specific gene expression profiles and potential overlaps in those in order to diagnose COPD, characterize its progression and determine the effect of drug treatment. METHOD: Global gene expression analysis was used for primary screening in order to obtain expression signatures of AMs and circulating MOs of COPD patients and healthy controls. The results of microarray analyses of AMs (20 controls and 26 COPD patients) and MOs (16 controls and 22 COPD patients) were confirmed and validated by real-time quantitative polymerase chain reaction. RESULTS: We have identified gene sets specifically associated with COPD in AMs and MOs. There were overlapping genes between the two cell types. Our data also show that COPD-specific gene expression signatures in AMs and MOs correlate with percent of predicted FEV(1). CONCLUSION: Disease-specific and overlapping gene expression signatures can be defined in lung-derived macrophages and also in circulating monocytes. Some of the validated expression changes in both cell types correlate with lung function and therefore could serve as biomarkers of disease progression.

Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization.

BACKGROUND: Hawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups. METHODS: We used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies. RESULTS: We obtained well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci. These are consistent with a previous morphology-based subgeneric classification of the genus. Despite the high heterogeneity of individual gene trees, we corroborate earlier evidence for the importance of hybridization in the evolution of Crataegus. Hybridization between subgenus Americanae and subgenus Sanguineae was documented for the origin of Sanguineae tetraploids, but not for a tetraploid Americanae species. This is also the first application of target capture probes designed with apple genome sequence. We successfully assembled 95% of 257 loci in Crataegus, indicating their potential utility across the genera of the apple tribe.

Antler development and coupled osteoporosis in the skeleton of red deer Cervus elaphus: expression dynamics for regulatory and effector genes.

Antlers of deer display the fastest and most robust bone development in the animal kingdom. Deposition of the minerals in the cartilage preceding ossification is a specific feature of the developing antler. We have cloned 28 genes which are upregulated in the cartilaginous section (called mineralized cartilage) of the developing ("velvet") antler of red deer stags, compared to their levels in the fetal cartilage. Fifteen of these genes were further characterized by their expression pattern along the tissue zones (i.e., antler mesenchyme, precartilage, cartilage, bone), and by in situ hybridization of the gene activities at the cellular level. Expression dynamics of genes col1A1, col1A2, col3A1, ibsp, mgp, sparc, runx2, and osteocalcin were monitored and compared in the ossified part of the velvet antler and in the skeleton (in ribs and vertebrae). Expression levels of these genes in the ossified part of the velvet antler exceeded the skeletal levels 10-30-fold or more. Gene expression and comparative sequence analyses of cDNAs and the cognate 5' cis-regulatory regions in deer, cattle, and human suggested that the genes runx2 and osx have a master regulatory role. GC-MS metabolite analyses of glucose, phosphate, ethanolamine-phosphate, and hydroxyproline utilizations confirmed the high activity of mineralization genes in governing the flow of the minerals from the skeleton to the antler bone. Gene expression patterns and quantitative metabolite data for the robust bone development in the antler are discussed in an integrated manner. We also discuss the potential implication of our findings on the deer genes in human osteoporosis research.

Gene expression patterns in the bone tissue of women with fibrous dysplasia.

Fibrous dysplasia is an isolated skeletal disorder caused by a somatic activating mutation of GNAS gene with abnormal unmineralized matrix overproduction and extensive undifferentiated bone cell accumulation in the fibro-osseous lesions. The aim of our investigation was to identify genes that are differently expressed in fibrous versus non-fibrous human bone and to describe the relationships between these genes using multivariate data analysis. Six bone tissue samples from female patients with fibrous dysplastia (FD) and seven bone tissue samples from women without FD (non-FD) were examined. The expression differences of selected 118 genes were analyzed by the TaqMan probe-based quantitative real-time RT-PCR system. The Mann-Whitney U-test indicated marked differences in the expression of 22 genes between FD and non-FD individuals. Nine genes were upregulated in FD women compared to non-FD ones and 18 genes showed a downregulated pattern. These altered genes code for minor collagen molecules, extracellular matrix digesting enzymes, transcription factors, adhesion molecules, growth factors, pro-inflammatory cytokines, and lipid metabolism-affected substrates. Canonical variates analysis demonstrated that FD and non-FD bone tissues can be distinguished by the multiple expression profile analysis of numerous genes controlled via a G-protein coupled pathway and BMP cascade as well as genes coding for extracellular matrix composing molecules. The remarkable changed gene expression profile observed in the fibrous dysplastic human bone tissue may provide further insight into the pathogenetic process of fibrous degeneration of bone.

Multilevel comparison of dendrograms: a new method with an application for genetic classifications.

Procedures are currently available for the evaluation of hierarchical classifications of produce tree dissimilarities or consensus dendrograms. Some tests of cluster validity operate by comparing all possible partitions from a tree with a reference partition. We propose an exhaustive search procedure to compare all partitions from one dendrogram with all partitions derived from the other to detect hierarchical levels at which the two dendrograms show maximum agreement. The method is illustrated using RAPD and microsatellite data in order to detect clones in reed populations. The utility of our approach is its ability to reveal extra information in different genetic data sets which would be hidden otherwise. The method is also useful in any field of science where hierarchical clustering is the main research tool and comparison of results is an objective. Artificial and actual dendrograms, together with randomly simulated trees were used to compare the performance of five classical coefficients of partition dissimilarity. The simulations showed that when meaningful group structure is lacking, then the five coefficients are in full disagreement, but they perform similarly otherwise.

[Changes of gene expression and its role in pathogenesis in fibrous and non-fibrous dysplastic bone tissues in women]. / A génexpresszió változásai és patogenetikai jelentôségük fibrosus dysplasiás és nem fibrosus dysplasiás nôk csontszövetében.

UNLABELLED: Fibrous dysplasia is an isolated skeletal disorder caused by a somatic activating mutation of GNAS1 gene with abnormal unmineralized matrix overproduction and extensive undifferentiated bone cell accumulation in fibro-osseous lesions. The aim of the investigation was to identify genes that are differently expressed in fibrous vs. non-fibrous human bone and to describe the relationships between these genes using multivariate data analysis. MATERIALS AND METHODS: Six bone tissue samples from fibrous dysplastic female patients and 7 bone tissue samples from non-fibrous dysplastic women were examined. The 6 female fibrous samples were taken from the fibrous dysplastic lesion itself while the control samples of 7 non-fibrous dysplastic females were taken from the femoral neck during the hip replacement procedure. The expression differences of selected 118 genes were analyzed in TaqMan probe based quantitative real-time RT-PCR system. RESULTS: The Mann-Whitney U test indicated significant differences in the expression of 27 genes of fibrous dysplasial and non fibrous dysplasial individuals (p≤0.05). Nine genes were significantly up-regulated in fibrous dysplasial women compared to non fibrous dysplasial ones and eighteen genes showed a down-regulated pattern. These significantly altered genes coding for minor collagen molecules, extracellular matrix digesting enzymes, transcription factors, adhesion molecules, growth factors, pro-inflammatory cytokines and lipid metabolism-affected substrates. Canonical variety analysis demonstrated that fibrous dysplastic and non fibrous dysplastic bone tissues can be distinguished by the multiple expression profile analysis of numerous genes controlled via a G-protein coupled pathway and BMP cascade as well as genes coding for extracellular matrix composing molecules. CONCLUSIONS: The significantly altered gene expression profile observed in the fibrous dysplastic human bone tissue may provide further insight into the pathogenetic process of fibrous degeneration of bone.

A study of community structure and beta diversity of epiphyllous liverwort assemblages in Sabah, Malaysian Borneo.

We evaluated the species richness and beta diversity of epiphyllous assemblages from three selected localities in Sabah, i.e. Mt. Silam in Sapagaya Forest Reserve, and Ulu Senagang and Mt. Alab in Crocker Range Park. A total of 98 species were found and a phytosociological survey was carried out based on the three study areas. A detailed statistical analysis including standard correlation and regression analyses, ordination of species and leaves using centered principal component analysis, and the SDR simplex method to evaluate the beta diversity, was conducted. Beta diversity is very high in the epiphyllous liverwort assemblages in Sabah, with species replacement as the major component of pattern formation and less pronounced richness difference. The community analysis of the epiphyllous communities in Sabah makes possible their detailed description and comparison with similar communities of other continents.

Targeted Mutational Profiling and a Powerful Risk Score as Additional Tools for the Diagnosis of Papillary Thyroid Cancer.

Nowadays, the complementary diagnostics based on the suspicious thyroid lesion specific mutational state analysis is indispensable in the clinical practice. We aimed to test and validate our novel 568-mutational hotspot panel (23 cancer-related genes) on papillary thyroid cancers (PTCs) and their tumor-free pairs to find the most powerful mutation pattern related to PTC. The sequencing method was carried on with Ion Torrent PGM on 67 thyroid tissue samples. The most commonly detected mutation was the BRAF c.1799 T > A in all non-classical PTC cases. We utilized a multivariate statistical method (CVA) to determine a discrimination score based on mutational data array and to assess malignancy risk. Based on variants, the BRAF gene has by far the highest indicative power, followed by TSHR and APC. We highlighted novel aspects of the mutational profile and genetic markers of PTC. CVA has correctly assigned most of the samples based on the mutation frequencies and different variables of the selected genes, with high analytical probabilities. The final goal is to set up a new comprehensive rule-in and rule-out test to support the clinical decision making mainly in inconclusive fine-needle aspiration biopsy cases.

Transcriptional profiling of immune system-related genes in postmenopausal osteoporotic versus non-osteoporotic human bone tissue.

The functional interaction between the immune system and bone metabolism has been established at both molecular and cellular levels. We have used non-parametric and multidimensional expression pattern analyses to determine significantly changed mRNA profile of immune system-associated genes in postmenopausal osteoporotic (OP) vs. non-osteoporotic (NOP) bone tissue. Seven bone tissue samples from OP patients and ten bone tissue samples from NOP women were examined in our study. The transcription differences of selected 44 genes were analyzed in Taqman probe-based quantitative real-time RT-PCR system. Mann-Whitney test indicated significantly down-regulated transcription activity of 3 genes (FCGR2A, NFKB1 and SCARA3) in OP bone tissue which have prominent role in (antibody) clearance, phagocytosis, pathogen recognition and inflammatory response. According to the canonical variates analysis results, the groups of postmenopausal OP and NOP women are separable by genes coding for cytokines, co-stimulators and cell surface receptors affected in innate immunity which have high discriminatory power. Based on the complex gene expression patterns in human bone cells, we could distinguish OP and NOP states from an immunological aspect. Our data may provide further insights into the changes of the intersystem crosstalk between the immune and skeletal systems, as well as into the local immune response in the altered microenvironment of OP bone.

Postmenopausal expression changes of immune system-related genes in human bone tissue.

INTRODUCTION: The molecular and cellular interactions between the immune system and bone tissue have been established. Sex hormone deficiency after menopause has multifunctional role by influencing growth, differentiation, and metabolism of the skeletal and the immune system. DISCUSSION: We have used nonparametric and multidimensional expression pattern analyses to determine significantly changed mRNA profile of immune system-associated genes in postmenopausal (POST) and premenopausal (PRE) nonosteoporotic bone. Ten bone tissue samples from POST patients and six bone tissue samples from PRE women were examined in our study. The transcription differences of the selected 50 genes were analyzed in TaqMan probe-based quantitative real-time reverse transcriptase polymerase chain reaction system. Mann-Whitney test indicated significantly downregulated transcription activity of three genes (CD14, HLA-A/MHCI, ITGAM/CD11b) and upregulated expression of six genes (C3, CD86/B7-2, IL-10, IL-6, TGFB3, TNFSF11/RANKL) in postmenopausal bone. According to the canonical variate analysis results, the groups of POST and PRE women are separable by genes coding for cytokines, costimulator molecules, and cell surface receptors involved in antigen presentation and T cell stimulation processes which have high discriminatory power. Based on a complex gene expression pattern analysis of human bone tissue, we could distinguish POST and PRE states from an immunological aspect. Our data might provide further insight into the changes of the intersystem crosstalk between immune and skeletal homeostasis, as well as local immune response in the altered microenvironment of postmenopausal bone.

Identifying novel genes involved in both deer physiological and human pathological osteoporosis.

Osteoporosis attacks 10% of the population worldwide. Humans or even the model animals of the disease cannot recover from porous bone. Regeneration in skeletal elements is the unique feature of our newly investigated osteoporosis model, the red deer (Cervus elaphus) stag. Cyclic physiological osteoporosis is a consequence of the annual antler cycle. This phenomenon raises the possibility to identify genes involved in the regulation of bone mineral density on the basis of comparative genomics between deer and human. We compare gene expression activity of osteoporotic and regenerating rib bone samples versus autumn dwell control in red deer by microarray hybridization. Identified genes were tested on human femoral bone tissue from non-osteoporotic controls and patients affected with age-related osteoporosis. Expression data were evaluated by Principal Components Analysis and Canonical Variates Analysis. Separation of patients into a normal and an affected group based on ten formerly known osteoporosis reference genes was significantly improved by expanding the data with newly identified genes. These genes include IGSF4, FABP3, FABP4, FKBP2, TIMP2, TMSB4X, TRIB, and members of the Wnt signaling. This study supports that extensive comparative genomic analyses, here deer and human, provide a novel approach to identify new targets for human diagnostics and therapy.

BOOL-AN: a method for comparative sequence analysis and phylogenetic reconstruction.

A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process. The method is based on algorithms generating mathematical representations directly from DNA/RNA or protein sequences, followed by the output of numerical (scalar or vector) and visual characteristics (graphs). The binary encoded sequence information is transformed into a compact analytical form, called the Iterative Canonical Form (or ICF) of Boolean functions, which can then be used as a generalized molecular descriptor. The method provides raw vector data for calculating different distance matrices, which in turn can be analyzed by neighbor-joining or UPGMA to derive a tree, or by principal coordinates analysis to get an ordination scattergram. The new method and the associated software for inferring phylogenetic trees are called the Boolean analysis or BOOL-AN.