A recently silenced, duplicate PgiC locus in Clarkia

Previous electrophoretic analysis showed that 17 diploid species of the wildflower Clarkia (Onagraceae) have two cytosolic isozymes of phosphoglucose isomerase (PGIC; EC 5.3.1.9), whereas 15 other diploid species have a single PGIC. Molecular studies revealed that the two isozymes in the former species are encoded by duplicate genes, PgiC1 and PgiC2, whereas the single isozyme in the latter is always encoded by PgiC1. Phylogenetic analysis of the nucleotide sequences implied that PgiC2 was silenced four times independently in the genus. Here we describe a psi PgiC2 from C. mildrediae, a species in which only PgiC1 is expressed. The discovery of the psi PgiC2 is significant because it confirms a formal prediction of the phylogenetic analysis. The psi PgiC2 includes 5,039 nucleotides corresponding to 18 of the 23 exons of PgiC, as well as the intervening introns and 3' nontranslated region. The absence of an increase of nucleotide substitutions in its "exons" suggests that the gene was silenced recently. The present study appears to be the first to establish that a specific duplicate gene locus regularly expressed in a group of related plant species has been silenced in one of them. The multiple independent silencings of PgiC2 suggest that it remained functional but inessential in ancestral lineages. We discuss the possibility that PgiC2 may have been preserved in these lineages by selection against mutants causing defective PGIC1- PGIC2 heterodimers.      

Homologies in Cambrian Onychophora

Marine animals related to Recent onychophorans form a significant component in Cambrian faunas. Twelve characters are analysed for homologies in the seven best known Cambrian onychophorans. New morphological evidence and homology analyses for several characters indicate an anteroposterior reversal of Hallucigenia and Microdictyon . Proposed expansion of the trunk in Microdietyon during compaction is rejected. A jaw is tentatively identified in Onychodictyon . The shape of the annulations and the disposition of the tenth leg pair in Aysheaia are reinterpreted, and the suggestion of two somites to the first appendage pair is rejected. A suggested morphocline may mirror the phylogeny of the group. The taxonomic confusion surrounding the supposed radiolarian family Eoconchariidae is cleared     

Latitudinal trends in plant‐pollinator interactions: are tropical plants more specialised?

The increase in richness of species and higher taxa going from higher to lower latitudes is one of the most studied global biogeographical patterns. Latitudinal trends in the interactions between species have, in contrast, hardly been studied at all, probably because recording interactions is much less straightforward than counting species. We have assembled two independent data sets which suggest that plant-pollinator interactions are not more ecologically specialised in the tropics compared to temperate latitudes. This is in contrast to a prevailing view that tropical ecological interactions tend towards higher specificity than their temperate counterparts.     

Interaction between platelet glycoprotein Ibalpha and filamin-1 is essential for glycoprotein Ib/IX receptor anchorage at high shear.

The interaction of the glycoprotein (GP) Ib-V-IX receptor complex with the membrane skeleton of platelets is dependent on a specific interaction between the cytoplasmic tail of GPIbalpha and filamin-1. This interaction has been proposed to regulate key aspects of platelet function, including the ligand binding of GPIb-V-IX and the ability of the cells to sustain adhesion to von Willebrand factor (vWf) under high shear. In this study we have examined sequences in the GPIbalpha intracellular domain necessary for interaction of the receptor with filamin-1. We have identified two adjacent sequences involving amino acids 557-568 and 569-579 of the GPIbalpha cytoplasmic domain that are critical for normal association between the receptor complex and filamin-1. Under flow conditions, Chinese hamster ovary (CHO) cells expressing these two mutant receptors exhibited an increase in translocation velocity that was associated with increased cell detachment from the vWf matrix at high shear. The shear-dependent acceleration in velocity of mutant Delta557-568 and Delta569-579 CHO cells was associated with a critical defect in receptor anchorage, evident from significant extraction of GPIb-IX from the CHO cell membrane at high shear. These studies define a critical role for amino acids within the 557-579 sequence of GPIbalpha for interaction with filamin-1.     

Statistical inference for valued-edge networks: the generalized exponential random graph model

Across the sciences, the statistical analysis of networks is central to the production of knowledge on relational phenomena. Because of their ability to model the structural generation of networks based on both endogenous and exogenous factors, exponential random graph models are a ubiquitous means of analysis. However, they are limited by an inability to model networks with valued edges. We address this problem by introducing a class of generalized exponential random graph models capable of modeling networks whose edges have continuous values (bounded or unbounded), thus greatly expanding the scope of networks applied researchers can subject to statistical analysis.     

Gas chromatographic determination of catecholestrogens following isolation by solid-phase extraction

A sensitive and specific assay for the determination of the catecholestrogens 2-hydroxyestradiol (2-OHE2) and 4-hydroxyestradiol (4-OHE2) using gas chromatography with electron-capture detection (GC–ECD) is described. The formation of 2- and 4-OHE2 was assessed following activation of 17β-estradiol in the microsomal fraction of female rat livers. The analytes were isolated by solid-phase extraction, derivatized to their heptafluorobutyryl esters with heptafluorobutyric acid anhydride, and subjected to solvent exchange prior to analysis; this resulted in minimal chromatographic interference, long column life, and stable derivatized analytes. Derivatized catechols were separated and confirmed with dual column chromatography (DB-5 and DB-608) and quantitated using GC–ECD. The DB-608 column was preferred for quantitation as it provided better 4-OHE2 resolution from interference. Key validation parameters for the assay include sensitivity, intra- and inter-assay precision, and accuracy. Instrument sensitivity and limits of detection (LOD) and quantitation (LOQ) were determined statistically from fortification data approaching expected limits. For 2-OHE2 and 4-OHE2, respective values for these parameters were; instrument sensitivities of 0.4 and 0.7 pg, LODs of 0.8 and 1.3 ng/mg, and LOQs of 2.6 and 4.3 ng/mg.     

JADE: An approach for interconnecting bioinformatics databases

To achieve the integration of biological data available on the World Wide Web and maintained in diverse sources such as GDB, Genbank or Acedb, we have developed a software called Jade. Jade allows programmers to create analytic tools and graphical user interfaces for one or more existing bioinformatics data sources. These tools can then be interchanged, compared and reused without making modifications in the data sources themselves. The system is implemented in the Java programming language and will run equally well on Macintosh, Windows or Unix workstations. Jade is free and can be used immediately by all interested parties.