Phylogeny of Drosophilinae (Diptera: Drosophilidae), with comments on combined analysis and character support

Drosophilidae (Diptera) is a diverse, cosmopolitan family of flies. Here, we present a combined analysis phylogeny of Drosophilinae, one of the two subfamilies of Drosophilidae, based on data from six different data partitions, including both molecular and morphological characters. Although our data show support for the monophyly of the Hawaiian Drosophilidae, and the subgenus Sophophora, neither the genus Drosophila nor the subgenus Drosophila is monophyletic. Partitioned Bremer support (PBS) indicates that morphological data taken from Grimaldi's monograph (Grimaldi, 1990a), as well as sequences from the mitochondrial (mt) 16S rDNA and the nuclear Adh gene, lend much support to our tree's topology. This is particularly interesting in the case of Grimaldi's data, since his published hypothesis conflicts with ours in significant ways. Our combined analysis cladogram phylogeny reflects the catch-all designation that the name Drosophila has become, in that the cladogram does not support the monophyly of either the genus or subgenus Drosophila.     

Physical mapping of genes in somatic cell radiation hybrids by comparative genomic hybridization to cDNA microarrays

Background  

Somatic cell mutants can be informative in the analysis of a wide variety of cellular processes. The use of map-based positional cloning strategies in somatic cell hybrids to analyze genes responsible for recessive mutant phenotypes is often tedious, however, and remains a major obstacle in somatic cell genetics. To fulfill the need for more efficient gene mapping in somatic cell mutants, we have developed a new DNA microarray comparative genomic hybridization (array-CGH) method that can rapidly and efficiently map the physical location of genes complementing somatic cell mutants to a small candidate genomic region. Here we report experiments that establish the validity and efficacy of the methodology.     

Phylogenetic analysis of 277 human G-protein-coupled receptors as a tool for the prediction of orphan receptor ligands

Background

G-protein-coupled receptors (GPCRs) are the largest and most diverse family of transmembrane receptors. They respond to a wide range of stimuli, including small peptides, lipid analogs, amino-acid derivatives, and sensory stimuli such as light, taste and odor, and transmit signals to the interior of the cell through interaction with heterotrimeric G proteins. A large number of putative GPCRs have no identified natural ligand. We hypothesized that a more complete knowledge of the phylogenetic relationship of these orphan receptors to receptors with known ligands could facilitate ligand identification, as related receptors often have ligands with similar structural features.

Results

A database search excluding olfactory and gustatory receptors was used to compile a list of accession numbers and synonyms of 81 orphan and 196 human GPCRs with known ligands. Of these, 241 sequences belonging to the rhodopsin receptor-like family A were aligned and a tentative phylogenetic tree constructed by neighbor joining. This tree and local alignment tools were used to define 19 subgroups of family A small enough for more accurate maximum-likelihood analyses. The secretin receptor-like family B and metabotropic glutamate receptor-like family C were directly subjected to these methods.

Conclusions

Our trees show the overall relationship of 277 GPCRs with emphasis on orphan receptors. Support values are given for each branch. This approach may prove valuable for identification of the natural ligands of orphan receptors as their relation to receptors with known ligands becomes more evident.     

Complex physiological and molecular processes underlying root gravitropism

Gravitropism allows plant organs to guide their growth in relation to the gravity vector. For most roots, this response to gravity allows downward growth into soil where water and nutrients are available for plant growth and development. The primary site for gravity sensing in roots includes the root cap and appears to involve the sedimentation of amyloplasts within the columella cells. This process triggers a signal transduction pathway that promotes both an acidification of the wall around the columella cells, an alkalinization of the columella cytoplasm, and the development of a lateral polarity across the root cap that allows for the establishment of a lateral auxin gradient. This gradient is then transmitted to the elongation zones where it triggers a differential cellular elongation on opposite flanks of the central elongation zone, responsible for part of the gravitropic curvature. Recent findings also suggest the involvement of a secondary site/mechanism of gravity sensing for gravitropism in roots, and the possibility that the early phases of graviresponse, which involve differential elongation on opposite flanks of the distal elongation zone, might be independent of this auxin gradient. This review discusses our current understanding of the molecular and physiological mechanisms underlying these various phases of the gravitropic response in roots.     

Regulation of alternative oxidase gene expression in soybean

Soybean (Glycine max cv. Stevens) suspension cells were used to investigate the expression of the alternative oxidase (Aox) multigene family. Suspension cells displayed very high rates of cyanide-insensitive respiration, but Aox3 was the only isoform detected in untreated cells. Incubation with antimycin A, citrate, salicylic acid or at low temperature (10 °C) specifically induced the accumulation of the Aox1 isoform. Aox2 was not observed under any conditions in the cells. Increases in Aox1 protein correlated with increases in Aox1 mRNA. Treatment of soybean cotyledons with norflurazon also induced expression of Aox1. Reactive oxygen species (ROS) were detected upon incubation of cells with antimycin, salicylic acid or at low temperature, but not during incubation with citrate. Aox1 induction by citrate, but not by antimycin, was prevented by including the protein kinase inhibitor staurosporine in the medium. The results suggest that multiple pathways exist in soybean to regulate expression of Aox genes and that Aox1 specifically is induced by a variety of stress and metabolic conditions via at least two independent signal transduction pathways.     

Abscisic acid and its influence on development of the embryonal root cap,storage product and secondary metabolite accumulation in hybrid larch somatic embryos

Somatic embryos of Larix × leptoeuropaea were grown on modified MSG media with 60 M abscisic acid (ABA). These were compared to control embryos raised on the same medium without ABA. Transmission electron microscopy demonstrated that zonation of polyphenol production as well as presence of extracellular mucilage was markedly different in embryos raised with and without ABA. Idioblasts were found in subepidermal and pith regions of hypocotyls and among the subepidermal cells of cotyledons in embryos matured on ABA, but not in embryos matured without ABA. The embryonal root caps of ABA-treated embryos had substantial deposition of lipids and proteins in both the column and inner pericolumn regions, but not in the outer layer of the pericolumn. Control embryos showed no accumulation of proteins or lipids, but an increase in polyphenol accumulation, which had spread to the epidermal and sub-epidermal layers of the cotyledons and hypocotyl. Starch accumulation was similar over the course of development in embryos treated with or without ABA. Using gas chromatography-selected reaction monitoring mass spectrometry, it was shown that concentrations of ABA averaged 186 ± 17 g g^–1 dry weight (DW) in embryos raised on medium supplemented with this plant growth regulator, versus an average concentration of 55 ± 19 g g^–1 DW in embryos raised in the absence of ABA. No difference in ABA concentration was found between the root cap and the rest of ABA-treated embryos.     

Endogenous levels of free and conjugated forms of auxin, cytokinins and abscisic acid during seed development in Douglas fir

Endogenous levels of free and conjugated forms of three classes of planthormones were quantified at various stages of megagametophyte development inDouglas fir. Megagametophytes were excised weekly from 8–16 weeks pastpollination (WPP), a period encompassing the central cell to the earlymaturation stage of seed development. The hormones indole-3 acetic acid (IAA),indole-3-aspartate (IAAsp), zeatin (Z), zeatin riboside (ZR), isopentenyladenine(iP), isopentenyladenosine (iPA), abscisic acid (ABA) and abscisic acid glucoseester (ABA-GE) were extracted, purified, fractionated by high- performanceliquid chromatography (HPLC), and then quantified using an enzyme-linkedimmunosorbent assay (ELISA) method. Z levels ranged from 0–25ng/g dry weight (DW) and were highest in megagametophytes at thecentral cell stage (8 WPP). During embryogenesis, Z levels peakedduring week 13. In contrast, the ZR conjugate was not detected over the periodstudied. The iP content of megagametophytes increased at 10 and 13WPP, while the iPA concentration increased at 13 WPP.Prior to fertilisation, IAA was highest in megagametophytes at 9WPP. During embryogenesis, the major IAA accumulations occurred at11, 13 and 15 WPP, the concentration ranging from 0–0.43g/g DW. IAAsp concentrations reached their highest level duringembryogenesis at 14 WPP. ABA content increased at 11 and 13WPP, with a concentration range of 0.1–13 g/gDW. In contrast, ABA-GE levels were relatively constant over the 9-weekperiod analyzed. The endogenous levels of plant hormones varied withmegagametophyte development and were associated with morphological changes.     

A hormonal role for endogenous opiate alkaloids: vascular tissues

The distribution of morphine-containing cells in the central nervous system, adrenal gland, and its presence in blood may serve to demonstrate that this signal molecule can act as a hormone besides its role in cell-to-cell signaling within the brain. This speculative review is the result of a literature evaluation with an emphasis on studies from our laboratory. Opioid peptides and opiate alkaloids have been found to influence cardiac and vascular function. They have also been reported to promote ischemic preconditioning protection in the heart. Given the presence of morphine and the novel mu(3) opiate receptor on vascular endothelial cells, including cardiac and vascular endothelial cells in the median eminence, it would appear that endogenous opiate alkaloids are involved in modulating cardiac function, possible at the hormonal level. This peripheral target tissue, via nitric oxide coupling to mu opiate receptors, may serve to down regulate the excitability of this tissue given the heart's high performance state as compared to that of the saphenous vein, a passive resistance conduit. With this in mind, morphine and other endogenous opiate alkaloids may function as a hormone.     

Contribution of the endoplasmic reticulum to the glucose-induced [Ca(2+)](c) response in mouse pancreatic islets

Thapsigargin (TG), a blocker of Ca(2+) uptake by the endoplasmic reticulum (ER), was used to evaluate the contribution of the organelle to the oscillations of cytosolic Ca(2+) concentration ([Ca(2+)](c)) induced by repetitive Ca(2+) influx in mouse pancreatic beta-cells. Because TG depolarized the plasma membrane in the presence of glucose alone, extracellular K(+) was alternated between 10 and 30 mM in the presence of diazoxide to impose membrane potential (MP) oscillations. In control islets, pulses of K(+), mimicking regular MP oscillations elicited by 10 mM glucose, induced [Ca(2+)](c) oscillations whose nadir remained higher than basal [Ca(2+)](c). Increasing the depolarization phase of the pulses while keeping their frequency constant (to mimic the effects of a further rise of the glucose concentration on MP) caused an upward shift of the nadir of [Ca(2+)](c) oscillations that was reproduced by raising extracellular Ca(2+) (to increase Ca(2+) influx) without changing the pulse protocol. In TG-pretreated islets, the imposed [Ca(2+)](c) oscillations were of much larger amplitude than in control islets and occurred on basal levels. During intermittent trains of depolarizations, control islets displayed mixed [Ca(2+)](c) oscillations characterized by a summation of fast oscillations on top of slow ones, whereas no progressive summation of the fast oscillations was observed in TG-pretreated islets. In conclusion, the buffering capacity of the ER in pancreatic beta-cells limits the amplitude of [Ca(2+)](c) oscillations and may explain how the nadir between oscillations remains above baseline during regular oscillations or gradually increases during mixed [Ca(2+)](c) oscillations, two types of response observed during glucose stimulation.     

Fine structure and activity of discrete RAG-HMG complexes on V(D)J recombination signals

Two lymphoid cell-specific proteins, RAG-1 and RAG-2, initiate V(D)J recombination by introducing DNA breaks at recombination signal sequences (RSSs). Although the RAG proteins themselves bind and cleave DNA substrates containing either a 12-RSS or a 23-RSS, DNA-bending proteins HMG-1 and HMG-2 are known to promote these processes, particularly with 23-RSS substrates. Using in-gel cleavage assays and DNA footprinting techniques, I analyzed the catalytic activity and protein-DNA contacts in discrete 12-RSS and 23-RSS complexes containing the RAG proteins and either HMG-1 or HMG-2. I found that both the cleavage activity and the pattern of protein-DNA contacts in RAG-HMG complexes assembled on 12-RSS substrates closely resembled those obtained from analogous 12-RSS complexes lacking HMG protein. In contrast, 23-RSS complexes containing both RAG proteins and either HMG-1 or HMG-2 exhibited enhanced cleavage activity and displayed an altered distribution of cleavage products compared to 23-RSS complexes containing only RAG-1 and RAG-2. Moreover, HMG-dependent heptamer contacts in 23-RSS complexes were observed. The protein-DNA contacts in RAG-RSS-HMG complexes assembled on 12-RSS or 23-RSS substrates were strikingly similar at comparable positions, suggesting that the RAG proteins mediate HMG-dependent heptamer contacts in 23-RSS complexes. Results of ethylation interference experiments suggest that the HMG protein is positioned 5' of the nonamer in 23-RSS complexes, interacting largely with the side of the duplex opposite the one contacting the RAG proteins. Thus, HMG protein plays the dual role of bringing critical elements of the 23-RSS heptamer into the same phase as the 12-RSS to promote RAG binding and assisting in the catalysis of 23-RSS cleavage.