Molecular Topology (molecular + topology)

Distribution by Scientific Domains

Selected Abstracts

Molecular systematics in the genus Clintonia and related taxa based on rbcL and matK gene sequence data

Kazuhiko Hayashi
Abstract In an attempt to elucidate the affinity and phylogeny of the disjunct North American,eastern Asian genus Clintonia, two chloroplast genes, rbcL and matK, were sequenced for all five species (Clintonia andrewsiana, Clintonia borealis, Clintonia umbellulata, Clintonia uniflora and Clintonia udensis). Similar sequence data sets for both genes supported the idea that a monophyly of Clintonia consists of two clades, one in eastern Asia and one in North America. The North American lineage resolves into an eastern group and a western group. There are surprisingly few site substitutions within these two genes, notwithstanding the wide morphological diversity of the genus. To root the Clintonia trees, Cardiocrinum (=Lilium) cordatum, Medeola virginiana, Scoliopus bigelovii and Scoliopus hallii were used as outgroup taxa. Similar topologies for Clintonia resulted when both the rbcL and matK gene sequences were combined. However, when an amino acid tree was generated for the matK sequence, all differences between the North American species were reduced to similarities due to synonymous codon sequences. Differentiation patterns of some selected morphological, karyological and embryological characters in Clintonia were also reviewed in comparison to the resulting molecular topologies. The unique, Clintonia -type megasporogenesis that produced identical, maternally derived, diploid zygotes and endosperm coupled to polyploid buffering provides a considerable constraint on variability. A search of possible sister genera to Clintonia was also attempted based on the molecular analyses and outgroup analysis, and Medeola virginiana from eastern North America turned out to be the closest relative found. [source]

What makes biochemical networks tick?

FEBS JOURNAL, Issue 19 2004
A graphical tool for the identification of oscillophores
In view of the increasing number of reported concentration oscillations in living cells, methods are needed that can identify the causes of these oscillations. These causes always derive from the influences that concentrations have on reaction rates. The influences reach over many molecular reaction steps and are defined by the detailed molecular topology of the network. So-called ,autoinfluence paths', which quantify the influence of one molecular species upon itself through a particular path through the network, can have positive or negative values. The former bring a tendency towards instability. In this molecular context a new graphical approach is presented that enables the classification of network topologies into oscillophoretic and nonoscillophoretic, i.e. into ones that can and ones that cannot induce concentration oscillations. The network topologies are formulated in terms of a set of uni-molecular and bi-molecular reactions, organized into branched cycles of directed reactions, and presented as graphs. Subgraphs of the network topologies are then classified as negative ones (which can) and positive ones (which cannot) give rise to oscillations. A subgraph is oscillophoretic (negative) when it contains more positive than negative autoinfluence paths. Whether the former generates oscillations depends on the values of the other subgraphs, which again depend on the kinetic parameters. An example shows how this can be established. By following the rules of our new approach, various oscillatory kinetic models can be constructed and analyzed, starting from the classified simplest topologies and then working towards desirable complications. Realistic biochemical examples are analyzed with the new method, illustrating two new main classes of oscillophore topologies. [source]

Biogeography of Plagiochila (Hepaticae): natural species groups span several floristic kingdoms

Henk Groth
Abstract Aim This paper presents a synthesis of our recent results regarding the biogeography of Plagiochila using a molecular approach, and documents intercontinental ranges within this largest genus of the hepatics. Methods A maximum likelihood analysis of sixty-one nrITS sequences of Plagiochila was performed and the molecular topology obtained was compared with morphological, phytochemical and geographical data. Results Our molecular data set allowed the identification of eleven Plagiochila sections, the majority of which cover at least two floristic kingdoms. Seven sections have species in Europe (sect. Arrectae, Carringtoniae, Fuscoluteae, Glaucescentes, Plagiochila, Rutilantes, Vagae). Plagiochila species from Atlantic Europe are usually close to or conspecific with neotropical taxa, whereas species widespread in Europe are closely related to Asian ones and not to those in the Neotropics. Plagiochila sect. Arrectae represents a neotropical , Atlantic European clade. The section is not closely related , as has often been suggested , to the morphologically similar sect. Zonatae from Asia and western North America. Sequence data show that the African P. integerrima and the neotropical P. subplana are members of the Asian sect. Cucullatae (sect. Ciliatae, syn. nov.), which becomes pantropical in distribution. An ITS sequence of P. boryana from Uganda confirms the Afro-American range of the primarily neotropical sect. Hylacoetes. Similarities in sporophyte morphology between the sect. Cucullatae and sect. Hylacoetes are the result of parallel evolution. Main conclusions Our results indicate that intercontinental ranges at section and species level are common in Plagiochila. Carl's (1931) subdivision of Plagiochila into sections restricted to one floristic kingdom is outdated. Biogeographical patterns in Plagiochila are not dissimilar to those of other groups of bryophytes but elucidation of the geographical ranges of the taxa requires a molecular approach. Contrary to earlier belief, most Plagiochila species from Atlantic Europe do not have close relatives in Asia but are conspecific with or closely related to species from tropical America. [source]

Prediction of Tyrosinase Inhibition Activity Using Atom-Based Bilinear Indices

CHEMMEDCHEM, Issue 4 2007
Yovani Marrero-Ponce Prof.
Abstract A set of novel atom-based molecular fingerprints is proposed based on a bilinear map similar to that defined in linear algebra. These molecular descriptors (MDs) are proposed as a new means of molecular parametrization easily calculated from 2D molecular information. The nonstochastic and stochastic molecular indices match molecular structure provided by molecular topology by using the kth nonstochastic and stochastic graph-theoretical electronic-density matrices, Mk and Sk, respectively. Thus, the kth nonstochastic and stochastic bilinear indices are calculated using Mk and Sk as matrix operators of bilinear transformations. Chemical information is coded by using different pair combinations of atomic weightings (mass, polarizability, vdW volume, and electronegativity). The results of QSAR studies of tyrosinase inhibitors using the new MDs and linear discriminant analysis (LDA) demonstrate the ability of the bilinear indices in testing biological properties. A database of 246 structurally diverse tyrosinase inhibitors was assembled. An inactive set of 412 drugs with other clinical uses was used; both active and inactive sets were processed by hierarchical and partitional cluster analyses to design training and predicting sets. Twelve LDA-based QSAR models were obtained, the first six using the nonstochastic total and local bilinear indices and the last six with the stochastic MDs. The discriminant models were applied; globally good classifications of 99.58 and 89.96,% were observed for the best nonstochastic and stochastic bilinear indices models in the training set along with high Matthews correlation coefficients (C) of 0.99 and 0.79, respectively, in the learning set. External prediction sets used to validate the models obtained were correctly classified, with accuracies of 100 and 87.78,%, respectively, yielding C values of 1.00 and 0.73. This subset contains 180 active and inactive compounds not considered to fit the models. A simulated virtual screen demonstrated this approach in searching tyrosinase inhibitors from compounds never considered in either training or predicting series. These fitted models permitted the selection of new cycloartane compounds isolated from herbal plants as new tyrosinase inhibitors. A good correspondence between theoretical and experimental inhibitory effects on tyrosinase was observed; compound CA6 (IC50=1.32,,M) showed higher activity than the reference compounds kojic acid (IC50=16.67,,M) and L -mimosine (IC50=3.68,,M). [source]