|
| ||
|
|
||
Calibration Points (calibration + point)
Selected AbstractsA linear three-center four electron bonding identity nucleophilic substitution at carbon, boron, and phosphorus.INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 7 2010A theoretical study in combination with van't Hoff modeling Abstract We studied various identity nucleophilic substitution reactions based on an SN2 reaction profile. With calculations and experimental geometries concerning the nature of the various complexes indicated as stable, intermediate, and transition state we were able to show the additional value of van't Hoff 's tetrahedron by changing its geometry via a trigonal pyramid into a trigonal bipyramid. The ratio of the apical and the corresponding tetrahedral bond distance is then 1.333. This value has been used in general as a calibration point for the understanding of the (in)stabilities of the complex formation on the SN2 reaction coordinate. The relevance of this approach has been also proved for enzymatic reactions focused on carbon and phosphorus substrates. Furthermore, it could be established that identity proton-in-line displacements are fully comparable with the relocation of carbon in a nucleophilic substitution reaction as Cl, + CH3Cl. The significance of this information will afford new insight in the dynamics of a linear three-center four-electron complex. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Molecular clocks keep dispersal hypotheses afloat: evidence for trans-Atlantic rafting by rodentsJOURNAL OF BIOGEOGRAPHY, Issue 2 2010Diane L. Rowe Abstract Aim, In order to resolve disputed biogeographical histories of biota with Gondwanan continental distributions, and to assess the null hypothesis of vicariance, it is imperative that a robust geological time-frame be established. As an example, the sudden and coincident appearance of hystricognath rodents (Rodentia: Hystricognathi) on both the African and South American continents has been an irreconcilable controversy for evolutionary biologists, presenting enigmas for both Gondwanan vicariance and Late Eocene dispersal hypotheses. In an attempt to resolve this discordance, we aim to provide a more robust phylogenetic hypothesis and improve divergence-date estimates, which are essential to assessing the null hypothesis of vicariance biogeography. Location, The primary centres of distribution are in Africa and South America. Methods, We implemented parsimony, maximum-likelihood and Bayesian methods to generate a phylogeny of 37 hystricognath taxa, the most comprehensive taxonomic sampling of this group to date, on the basis of two nuclear gene regions. To increase phylogenetic resolution at the basal nodes, these data were combined with previously published data for six additional nuclear gene regions. Divergence dates were estimated using two relaxed-molecular-clock methods, Bayesian multidivtime and nonparametric rate smoothing. Results, Our data do not support reciprocal monophyly of African and South American lineages. Indeed, Old World porcupines (i.e. Hystricomorpha) appear to be more closely related to New World lineages (i.e. Caviomorpha) than to other Old World families (i.e. Bathyergidae, Petromuridae and Thryonomyidae). The divergence between the monophyletic assemblage of South American lineages and its Old World ancestor was estimated to have occurred c. 50 Ma. Main conclusions, Our phylogenetic hypothesis and divergence-date estimates are strongly at odds with Gondwanan-vicariance isolating mechanisms. In contrast, our data suggest that transoceanic dispersal has played a significant role in governing the contemporary distribution of hystricognath rodents. Molecular-clock analyses imply a trans-Tethys dispersal event, broadly confined to the Late Cretaceous, and trans-Atlantic dispersal within the Early Eocene. Our analyses also imply that the use of the oldest known South American rodent fossil as a calibration point has biased molecular-clock inferences. [source] Towards a universal product ion mass spectral library , reproducibility of product ion spectra across eleven different mass spectrometersRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 12 2008Chris Hopley Product ion spectra produced by collision-induced dissociation (CID) in tandem mass spectrometry experiments can differ markedly between instruments. There have been a number of attempts to standardise the production of product ion spectra; however, a consensus on the most appropriate approach to the reproducible production of spectra has yet to be reached. We have previously reported the comparison of product ion spectra on a number of different types of instruments , a triple quadrupole, two ion traps and a Fourier transform ion cyclotron resonance mass spectrometer (Bristow AWT, Webb KS, Lubben AT, Halket JM. Rapid Commun. Mass Spectrom. 2004; 18: 1). The study showed that a high degree of reproducibility was achievable. The goal of this study was to improve the comparability and reproducibility of CID product ion mass spectra produced in different laboratories and using different instruments. This was carried out experimentally by defining a spectral calibration point on each mass spectrometer for product ion formation. The long-term goal is the development of a universal (instrument independent) product ion mass spectral library for the identification of unknowns. The spectra of 48 compounds have been recorded on eleven mass spectrometers: six ion traps, two triple quadrupoles, a hybrid triple quadrupole, and two quadrupole time-of-flight instruments. Initially, 4371 spectral comparisons were carried out using the data from eleven instruments and the degree of reproducibility was evaluated. A blind trial has also been carried out to assess the reproducibility of spectra obtained during LC/MS/MS. The results suggest a degree of reproducibility across all instrument types using the tuning point technique. The reproducibility of the product ion spectra is increased when comparing the tandem in time type instruments and the tandem in space instruments as two separate groups. This may allow the production of a more limited, yet useful, screening library for LC/MS/MS identification using instruments of the same type from different manufacturers. Copyright © 2008 John Wiley & Sons, Ltd. [source] When Thailand was an island , the phylogeny and biogeography of mite harvestmen (Opiliones, Cyphophthalmi, Stylocellidae) in Southeast AsiaJOURNAL OF BIOGEOGRAPHY, Issue 6 2010Ronald M. Clouse Abstract Aim, To develop a comprehensive explanation for the biological diversity of Southeast Asia, especially in the Wallacea and Sundaland regions. This study focuses on a group of arachnids, mite harvestmen, which are thought to be an extremely old group of endemic animals that have been present in the region since most of its land supposedly formed part of the northern rim of the supercontinent Gondwana. Location, Eastern Himalayas, Thai-Malay Peninsula, Sumatra, Borneo, Java, Sulawesi, and New Guinea. Methods Approximately 5.6 kb of sequence data were obtained from 110 South-east Asian Cyphophthalmi specimens. Phylogenetic analyses were conducted under a variety of methods and analytical parameters, and the optimal tree was dated using calibration points derived from fossil data. Event based and paralogy-free subtree biogeographical analyses were conducted. Results, The Southeast Asian family Stylocellidae was recovered as monophyletic, arising on what is now the Thai-Malay Peninsula and diversifying into three main clades. One clade (Meghalaya, here formally placed in Stylocellidae) expanded north as far as the eastern Himalayas, a second clade entered Borneo and later expanded back across the Sundaland Peninsula to Sumatra, and a third clade expanded out of Borneo into the entire lower part of Sundaland. Molecular dating suggested that Stylocellidae separated from other Cyphophthalmi 295 Ma and began diversifying 258 Ma, and the lineage that inhabits mostly Borneo today began diversifying between 175 and 150 Ma. Main conclusions, The topology and molecular dating of our phylogenetic hypothesis suggest that Stylocellidae originated on Gondwana, arrived in Southeast Asia via the Cimmerian palaeocontinent, and subsequently diversified north, then south. Their present distribution in the Indo-Malay Archipelago is explained largely by a diversification over the Sundaland Peninsula before western Sulawesi departed and the peninsula was extensively inundated. [source] Rhizocarpon calibration curve for the Aoraki/Mount Cook area of New Zealand,JOURNAL OF QUATERNARY SCIENCE, Issue 4 2005Thomas V. Lowell Abstract Development of Rhizocarpon growth curve from the Aoraki/Mount Cook area of New Zealand provides a means to assess Little Ice Age glacier behaviour and suggests approaches that have wider application. Employing a sampling strategy based on large populations affords the opportunity to assess which of various metrics (e.g. single largest, average of five largest, mean of an entire population) best characterise Rhizocarpon growth patterns. The 98% quantile from each population fitted with a quadric curve forms a reliable representation of the growth pattern. Since this metric does not depend on the original sample size, comparisons are valid where sample strategy must be adapted to local situations or where the original sample size differs. For the Aoraki/Mount Cook area a surface 100 years old will have a 98% quantile lichen diameter of 34.3,mm, whereas a 200-year-old surface will have a lichen diameter of 73.7,mm. In the Southern Alps, constraints from the age range of calibration points, the flattening of the quadric calibration curve and ecological factors limit the useful age range to approximately 250 years. Copyright © 2005 John Wiley & Sons, Ltd. [source] Phylogeographical structure and temporal complexity in American sweetgum (Liquidambar styraciflua; Altingiaceae)MOLECULAR ECOLOGY, Issue 17 2008ASHLEY B. MORRIS Abstract Eastern North American plant biogeography has traditionally focused on two primary issues: (i) the location of temperate Pleistocene refugia and their proximity to the southern margin of the ice sheet during the last glacial maximum, and (ii) the origin of the temperate element of northern Latin America. While numerous population genetic and phylogeographical studies have focused on the first issue, few (if any) have considered the second. We addressed these issues by surveying 117 individuals from 24 populations of Liquidambar styraciflua (American sweetgum; Altingiaceae) across the southeastern USA, eastern Mexico, and Guatemala, using more than 2200 bp of chloroplast DNA sequence data. To specifically address the issue of timing, we estimated intraspecific divergence times on the basis of multiple fossil-based calibration points, using taxa from Altingiaceae (Liquidambar and Altingia) and Hammamelidaceae (Hamamelis) as outgroups. More than half of the sampled localities exhibited multiple haplotypes. Remarkably, the greatest variation was observed within the USA, with Mexico and Guatemala sharing widespread haplotypes with Texas, Mississippi, Kentucky, Ohio, and northern Virginia. This lack of differentiation suggests shared ancestral polymorphisms, and that the genetic signal we observed is older than the disjunction itself. Our data provide support for previously proposed hypotheses of Pleistocene refugia in peninsular Florida and along the eastern Atlantic, but also for deeper divergences (~8 million years ago) within the USA. These patterns reflect a dynamic biogeographical history for eastern North American trees, and emphasize the importance of the inclusion of a temporal component in any phylogeographical study. [source] [2H/H] Isotope ratio analyses of [2H5]cholesterol using high-temperature conversion elemental analyser isotope-ratio mass spectrometry: determination of cholesterol absorption in normocholesterolemic volunteersRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 3 2004Jean-Philippe Godin This paper validates the use of high-temperature conversion elemental analyser isotope-ratio mass spectrometry (TC-EA/IRMS) for measuring the [2H/H] enrichment of plasma [2H5]cholesterol. From a molecular point of view, the free cholesterol is initially separated from plasma by thin-layer chromatography (TLC) and then injected onto the TC-EA reactor which converts cholesterol molecules into CO and H2 gases. The slope of the curve of the experimental mole percent excess (MPE(exp.)) versus MPE(theor.) was very close to 1, demonstrating that no significant isotopic fractionation was observed during all processing of the samples (i.e., isolation of plasma free cholesterol by TLC and pyrolysis in the TC-EA reactor). Excellent linearity (r2,=,0.9994, n,=,4) of , (,) of [2H/H] isotopic measurements versus mole percent (MP) was assessed over the range 0 to 0.1 MP. The precision of the [2H/H] measurement, evaluated with two calibration points processed with TLC, was ,2HV-SMOW,=,,192.5,±,3.4, and ,2HV-SMOW,=,,136.9,±,2.9,. The standard deviations of the within-assay and between-assay repeatabilities of the analytical process, evaluated using the quality control (QC) of plasma samples, were 4.6 and 6.1,, respectively. Plant sterols are known to reduce cholesterol absorption and therefore were used as a positive control in a clinical study performed with normocholesterolemic volunteers. This present method produces biological results consistent with those already reported in the literature. Copyright © 2004 John Wiley & Sons, Ltd. [source] | |||||||||||||