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PubMed2003

Sub-grouping of Plasmodium falciparum 3D7 var genes based on sequence analysis of coding and non-coding regions.

BACKGROUND: The variant surface antigen family Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors. The sequence diversity and organization of the 3D7 PfEMP1 repertoire was investigated on the basis of the complete genome sequence. METHODS: Using two tree-building methods we analysed the coding and non-coding sequences of 3D7 var and rif genes as well as var genes of other parasite strains. RESULTS: var genes can be sub-grouped into three major groups (group A, B and C) and two intermediate groups B/A and B/C representing transitions between the three major groups. The best defined var group, group A, comprises telomeric genes transcribed towards the telomere encoding PfEMP1s with complex domain structures different from the 4-domain type dominant of groups B and C. Two sequences belonging to the var1 and var2 subfamilies formed independent groups. A rif subgroup transcribed towards the centromere was found neighbouring var genes of group A such that the rif and var 5' regions merged. This organization appeared to be unique for the group A var genes CONCLUSION: The grouping of var genes implies that var gene recombination preferentially occurs within var gene groups and it is speculated that the groups reflect a functional diversification evolved to cope with the varying conditions of transmission and host immune response met by the parasite.

Animals↗

PubMed1999

Molecular differentiation and phylogeny of entomopathogenic nematodes (rhabditida: heterorhabditidae) based on ND4 gene sequences of Mitochondrial DNA.

We determined partial ND4 gene sequences of mitochondrial DNA from 15 heterorhabditid nematode isolates, representing 5 species collected from different regions of the world, by using polymerase chain reaction (PCR) and direct-sequencing of PCR products. Aligned nucleotide as well as amino acid sequences were used to differentiate nematode species by comparing sequence divergence and to infer phylogeny of the nematodes by using maximum parsimony and likelihood methods. Robustness of our phylogenetic trees was checked by bootstrap tests. The 15 nematode isolates can be divided into 7 haplotypes based on DNA sequences. On a larger scale, the sequence divergence revealed 4 distinct groups corresponding to 4 described species. No sequence divergence was detected from 5 isolates of Heterorhabditis bacteriophora or between Heterorhabditis marelatus to Heterorhabditis hepialius. Our sequence data yielded phylogenetic trees with identical topologies when different tree-building methods were used. Most relationships were also confirmed by using amino acid sequences in maximum parsimony analysis. Our molecular phylogeny of Heterorhabditis species support an existing taxonomy that is based largely on morphology and the sequence divergence of the ND4 gene permits species identification.

Amino Acid Sequence↗

PubMed2001

Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support.

We have investigated the effects of different among-site rate variation models on the estimation of substitution model parameters, branch lengths, topology, and bootstrap proportions under minimum evolution (ME) and maximum likelihood (ML). Specifically, we examined equal rates, invariable sites, gamma-distributed rates, and site-specific rates (SSR) models, using mitochondrial DNA sequence data from three protein-coding genes and one tRNA gene from species of the New Zealand cicada genus Maoricicada. Estimates of topology were relatively insensitive to the substitution model used; however, estimates of bootstrap support, branch lengths, and R-matrices (underlying relative substitution rate matrix) were strongly influenced by the assumptions of the substitution model. We identified one situation where ME and ML tree building became inaccurate when implemented with an inappropriate among-site rate variation model. Despite the fact the SSR models often have a better fit to the data than do invariable sites and gamma rates models, SSR models have some serious weaknesses. First, SSR rate parameters are not comparable across data sets, unlike the proportion of invariable sites or the alpha shape parameter of the gamma distribution. Second, the extreme among-site rate variation within codon positions is problematic for SSR models, which explicitly assume rate homogeneity within each rate class. Third, the SSR models appear to give severe underestimates of R-matrices and branch lengths relative to invariable sites and gamma rates models in this example. We recommend performing phylogenetic analyses under a range of substitution models to test the effects of model assumptions not only on estimates of topology but also on estimates of branch length and nodal support.

Animals↗

PubMed2002

Genetic divergence within the Drosophila mayaguana subcluster, a closely related triad of Caribbean species in the repleta species group.

The mayaguana triad of the Drosophila repleta species group includes D. mayaguana, D. straubae, and D. parisiena, the latter two of which are very similar when examined morphologically. Many morphological characters used to define these taxa are quantitative and overlap substantially among some forms--it is only through suites of such characters that species can be identified. We apply Population Aggregation Analysis and tree building methods to five rapidly evolving gene regions--the mitochondrial AT rich region and the nuclear acetylcholinesterase, hunchback, mastermind, and vestigial loci to test the morphological species delineations within the morphocryptic mayaguana triad. We find that D. mayaguana is diagnosable using DNA sequences, but the other two species form a non-diagnosable paraphyletic assemblage. A single ecological factor, oviposition substrate, is an important diagnostic character distinguishing D. straubae from D. parisiena, highlighting the importance of examining a diverse array of data (morphological, molecular, ecological, and behavioral) when defining species limits.

Animals↗

PubMed1992

[Injuries following a hurricane in Nordmøre].

In this article we describe the efforts of local authorities to detect and treat casualties caused by a hurricane that struck the west coast of Norway January 1st, 1992 and prevent further injuries. Wind velocity exceeded 100 knots (117 mph), the strongest ever recorded in Norway. The damage to buildings, trees and power lines was so devastating that the Nordmøre area, with approximately 50,000 inhabitants, was left without electricity for five days. Altogether 56 casualties were reported by physicians and the local hospital (one death, caused by hypothermia and exhaustion, and six admissions to hospital) in the period 1-5 January. Nine old people suffered injuries by falling in the dark in their houses, and ten men were injured during repair work.

Adult↗

PubMed2004

[A group of new experiments on molecular evolution].

This paper presents a group of new experiments on molecular evolution. It allows students to get acquaint with the basic process of the reconstruction of phylogenetic tree using DNA or protein sequences, and to acquire the correct viewpoint how to affect the result of reconstruction when different tree-building methods, materials and parameters were used. This group of experiments are also characteristic of the opening and exploring, which accords with the direction and demand of experimental teaching reform.

Animals↗

PubMed2006

Inference of molecular phylogeny of Sarcocystis felis (Sarcocystidae) from cats based on nuclear-encoded ribosomal gene sequences.

The phylogenetic position of four clinical isolates of Sarcocystis felis was assessed using ssurRNA and ITS1 gene sequences in the context of a wide array of other Sarcocystis sp. Phylogenetic reconstructions using neighbour-joining and maximum parsimony methods generated identical tree topologies with strong support values at each node. High ssurRNA sequence similarity (> or =99%) and the resulting phylogeny demonstrated that S. felis and S. neurona are significantly closely related to each other. The two Sarcocystis formed a monophyletic group distinct from the other Sarcocystis sp., irrespective of the alignment algorithms or tree-building method used. The absolute (100%) identity of ssurRNA sequences of sarcocysts and sporocysts obtained from one cat raised the question regarding the cat's role as a potential intermediate host besides its known role as a definitive host of S. felis. On the other hand, S. felis sarcocyst DNA sequence was found to be quite dissimilar over the ITS1 region when compared to S. neurona. These findings indicated that using sequences from two different genetic loci provided a stronger comparative basis than would have been possible using either one.

Animals↗

PubMed1988

Phylogenetic relationships of the apicomplexan protist Sarcocystis as determined by small subunit ribosomal RNA comparison.

Reverse transcription of total cellular RNA was used to obtain the partial nucleotide sequence of the small subunit ribosomal RNA (srRNA) of Sarcocystis gigantea. The sequence was compared with the homologous sequences of 24 other eukaryotes. Phylogenetic analysis of the semiconserved regions by 4 different tree-building methods using bacteria as an outgroup all concur in showing monophyly of Sarcocystis gigantea and Toxoplasma gondii to the exclusion of all other taxa for which homologous sequences are available.

Animals↗

PubMed1998

[Dispersion modelling or organic particles from animal stalls and other comparable installations].

Different numerical models have been used to study air flow and dispersion in the surrounding of stables. The results show a strong dependency on the configuration of the direct neighborhood (other buildings, trees) and on the meteorological conditions (windspeed, thermal stratification). The findings demonstrate the inability of simple models like the Gaussian model in complex situations.

Air Pollutants, Occupational↗

PubMed1999

Biomechanical properties of the trunk of the devil's walking stick (Aralia spinosa; Araliaceae) during the crown-building phase: implications for tree architecture.

During the crown-building phase, the mechanical architecture of the trunk of Aralia spinosa exhibits considerable ontogenetic variation. All trunks were tapered along their length, and taper was dependent on both ramet size and age; older, larger trunks were more tapered than younger, smaller trunks. Trunk specific gravity, % bark, wood, and pith exhibited considerable inter- and intra-ramet variation. Specific gravity increased with both increasing ramet size and age, and declined acropetally in the majority of ramets sampled. Wood specific gravity was generally unrelated to ramet size, age, or position along the length of the trunk. Percent wood increased while % pith decreased with increasing ramet size and age. There was no relationship between % bark and either ramet size or age. Both % bark and % wood tended to decline acropetally, while % pith increased acropetally. On average, 47% of the variation in specific gravity could be attributed to % wood, while 77% could be attributed to % pith. Percent bark accounted for only 14% of the variation in specific gravity. We suggest that the relatively pithy trunk of Aralia spinosa (average range: 4-15%) allows for rapid height growth, but imposes severe constraints on crown architecture and the maximum size attainable by this species.

Journal Article↗

PubMed2004

RBT--a tool for building refined Buneman trees.

SUMMARY: We have developed a tool implementing an efficient algorithm for refined Buneman tree reconstruction. The algorithm--which has the same complexity as the neighbour-joining method and the (plain) Buneman tree construction--enables refined Buneman tree reconstruction on large taxa sets. AVAILABILITY: The source code for RBT, written in Java, is available under the GNU Public License (GPL) at http://www.birc.dk/Software/RBT CONTACT: besen@daimi.au.dk.

Algorithms↗

PubMed2006

PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences.

MOTIVATION: To construct a multiple sequence alignment (MSA) of a large number (> approximately 10,000) of sequences, the calculation of a guide tree with a complexity of O(N2) to O(N3), where N is the number of sequences, is the most time-consuming process. RESULTS: To overcome this limitation, we have developed an approximate algorithm, PartTree, to construct a guide tree with an average time complexity of O(N log N). The new MSA method with the PartTree algorithm can align approximately 60,000 sequences in several minutes on a standard desktop computer. The loss of accuracy in MSA caused by this approximation was estimated to be several percent in benchmark tests using Pfam. AVAILABILITY: The present algorithm has been implemented in the MAFFT sequence alignment package (http://align.bmr.kyushu-u.ac.jp/mafft/software/). SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.

Algorithms↗

PubMed2006

Building the component tree in quasi-linear time.

The level sets of a map are the sets of points with level above a given threshold. The connected components of the level sets, thanks to the inclusion relation, can be organized in a tree structure, that is called the component tree. This tree, under several variations, has been used in numerous applications. Various algorithms have been proposed in the literature for computing the component tree. The fastest ones (considering the worst-case complexity) have been proven to run in O(n ln(n)). In this paper, we propose a simple to implement quasi-linear algorithm for computing the component tree on symmetric graphs, based on Tarjan's union-find procedure. We also propose an algorithm that computes the n most significant lobes of a map.

Algorithms↗

PubMed2005

Do orthologous gene phylogenies really support tree-thinking?

BACKGROUND: Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes. RESULTS: Heat map analyses were used to investigate the congruence of orthologues in four datasets (archaeal, bacterial, eukaryotic and alpha-proteobacterial). We conclude that we simply cannot determine if a large portion of the genes have a common history. In addition, none of these datasets can be considered free of lateral gene transfer. CONCLUSION: Our phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.

Algorithms↗

PubMed2005

Improved detection of prostate cancer using classification and regression tree analysis.

PURPOSE: To build a decision tree for patients suspected of having prostate cancer using classification and regression tree (CART) analysis. PATIENTS AND METHODS: Data were uniformly collected on 1,433 referred men with a serum prostate-specific antigen (PSA) levels of < or = 10 ng/mL who underwent a prostate biopsy. Factors analyzed included demographic, laboratory, and ultrasound data (ie, hypoechoic lesions and PSA density [PSAD]). Twenty percent of the data was randomly selected and reserved for study validation. CART analysis was performed in two steps, initially using PSA and digital rectal examination (DRE) alone and subsequently using the remaining variables. RESULTS: CART analysis selected a PSA cutoff of more than 1.55 ng/mL for further work-up, regardless of DRE findings. CART then selected the following subgroups at risk for a positive biopsy: (1) PSAD more than 0.165 ng/mL/cc; (2) PSAD < or = 0.165 ng/mL/cc and a hypoechoic lesion; (3) PSAD < or = 0.165 ng/mL/cc, no hypoechoic lesions, age older than 55.5 years, and prostate volume < or = 44.0 cc; and (4) PSAD < or = 0.165 ng/mL/cc, no hypoechoic lesions, age older than 55.5 years, and 50.25 cc less than prostate volume < or = 80.8 cc. In the validation data set, specificity and sensitivity were 31.3% and 96.6%, respectively. Cancers that were missed by the CART were Gleason score 6 or less in 93.4% of cases. Receiver operator characteristic curve analysis showed that CART and logistic regression models had similar accuracy (area under the curve = 0.74 v 0.72, respectively). CONCLUSION: Application of CART analysis to the prostate biopsy decision results in a significant reduction in unnecessary biopsies while retaining a high degree of sensitivity when compared with the standard of performing a biopsy of all patients with an abnormal PSA or DRE.

Adult↗

PubMed2000

Forecasting physicochemical variables by a classification tree method. Application to the Berre Lagoon (south France).

The dynamics of the "Etang de Berre", a brackish lagoon situated close to the French Mediterranean sea coast, is strongly disturbed by freshwater inputs coming from an hydroelectric power station. The system dynamics has been described as a sequence of daily typical states from a set of physicochemical variables such as temperature, salinity and dissolved oxygen rates collected over three years by an automatic sampling station. Each daily pattern summarizes the evolution, hour by hour of the physicochemical variables. This article presents results of forecasts of the states of the system subjected to the simultaneous effects of meteorological conditions and freshwater releases. We recall the main step of the classification tree method used to build up the predictive model (Classification and Regression Trees, Breiman et al., 1984) and we propose a transfer procedure in order to test the stability of the model. Results obtained on the Etang de Berre data set allow us to describe and predict the effects of the environmental variables on the system dynamics with a margin of error. The transfer procedure applied after the tree building process gives a maximum gain in prediction accuracy of about 15%.

Environmental Monitoring↗

PubMed2001

Finding the right decision tree's induction strategy for a hard real world problem.

Decision trees have been already successfully used in medicine, but as in traditional statistics, some hard real world problems can not be solved successfully using the traditional way of induction. In our experiments we tested various methods for building univariate decision trees in order to find the best induction strategy. On a hard real world problem of the Orthopaedic fracture data with 2637 cases, described by 23 attributes and a decision with three possible values, we built decision trees with four classical approaches, one hybrid approach where we combined neural networks and decision trees, and with an evolutionary approach. The results show that all approaches had problems with either accuracy, sensitivity, or decision tree size. The comparison shows that the best compromise in hard real world problem decision trees building is the evolutionary approach.

Algorithms↗

PubMed1999

The influence of class discretization to attribute hierarchy of decision trees.

Decision support systems that help physicians are becoming very important part of medical decision making. They are based on different models and the best of them are providing an explanation together with an accurate, reliable and quick response. One of the most viable among decision-making models is the concept of decision trees, already successfully used for many medical decision making purposes. Although effective and reliable, the traditional decision tree construction approach still contains several deficiencies. Therefore we decided to develop and compare several decision supporting models, each of them built with different discretization of attributes and decision classes. For the construction of decision trees we used MtDeciT, in our laboratory developed tool for building decision trees using the classical induction method. All solutions were evolved for determining the influence of basic properties of child and his/her parents to length of successful breastfeeding. A comparison between developed models and obtained results has shown that the way of discretization obviously plays a great role in the reliable and accurate real-world medical decision making.

Adult↗