Mitochondrial genome and a nuclear gene indicate a novel phylogenetic position of deep-sea tube-eye fish (Stylephoridae)

The rare, monotypic deep-sea fish family Stylephoridae has long been considered a member of the order Lampridiformes (opahs, velifers, ribbonfishes), and no systematic ichthyologist has questioned its placement within the order for over 80 years. Recently three individuals of Stylephorus chordatus were collected from different oceans, and we sequenced the whole mitochondrial genome and a partial nuclear recombination activating gene 1 (RAG1) gene sequences for each specimen. We aligned these sequences with those available from higher teleosts, including representative lampridiforms, and constructed two separate datasets from the sequences. The resulting trees derived from partitioned Bayesian analyses strongly indicated that S. chordatus is not a lampridiform but is closely related to the order Gadiformes (cod and their relatives). Lampridiformes is diagnosed on the basis of four synapomorphies, three of which are correlated with the rare and possibly unique ability to extend both the maxilla and premaxilla as a unit during feeding. Stylephorus also possesses such unique ability, but lacks two and possibly three of the four synapomorphies, suggesting that further morphological analysis is needed. Considering its unique morphologies with no indication of affinities within Gadiformes (or any other presently recognized order), the present results warrant a recognition of the new order for S. chordatus in fish systematics.     

Enabling high-throughput data management for systems biology: the Bioinformatics Resource Manager

The Bioinformatics Resource Manager (BRM) is a software environment that provides the user with data management, retrieval and integration capabilities. Designed in collaboration with biologists, BRM simplifies mundane analysis tasks of merging microarray and proteomic data across platforms, facilitates integration of users' data with functional annotation and interaction data from public sources and provides connectivity to visual analytic tools through reformatting of the data for easy import or dynamic launching capability. BRM is developed using Java and other open-source technologies for free distribution. AVAILABILITY: BRM, sample data sets and a user manual can be downloaded from http://www.sysbio.org/dataresources/brm.stm.     

Evolution and origin of sympatric shallow-water morphotypes of Lake Trout,Salvelinus namaycush,in Canada's Great Bear Lake

Range expansion in north-temperate fishes subsequent to the retreat of the Wisconsinan glaciers has resulted in the rapid colonization of previously unexploited, heterogeneous habitats and, in many situations, secondary contact among conspecific lineages that were once previously isolated. Such ecological opportunity coupled with reduced competition likely promoted morphological and genetic differentiation within and among post-glacial fish populations. Discrete morphological forms existing in sympatry, for example, have now been described in many species, yet few studies have directly assessed the association between morphological and genetic variation. Morphotypes of Lake Trout, Salvelinus namaycush, are found in several large-lake systems including Great Bear Lake (GBL), Northwest Territories, Canada, where several shallow-water forms are known. Here, we assess microsatellite and mitochondrial DNA variation among four morphotypes of Lake Trout from the five distinct arms of GBL, and also from locations outside of this system to evaluate several hypotheses concerning the evolution of morphological variation in this species. Our data indicate that morphotypes of Lake Trout from GBL are genetically differentiated from one another, yet the morphotypes are still genetically more similar to one another compared with populations from outside of this system. Furthermore, our data suggest that Lake Trout colonized GBL following dispersal from a single glacial refugium (the Mississippian) and support an intra-lake model of divergence. Overall, our study provides insights into the origins of morphological and genetic variation in post-glacial populations of fishes and provides benchmarks important for monitoring Lake Trout biodiversity in a region thought to be disproportionately susceptible to impacts from climate change.     

Bone Morphogenetic Protein functions as a context-dependent angiogenic cue in vertebrates

Bone Morphogenetic Protein (BMP) signaling has been implicated in diverse biological processes. Although how BMP signaling regulates behaviors of endothelial cells during angiogenesis are not fully understood, increasing evidence indicate functions of BMP signaling components are essential in developmental and pathological angiogenesis. Here we review recent advances in delineating the functions of BMP signaling during angiogenesis. In addition, we discuss downstream pathways that transduce BMP signaling in endothelial cells, and factors that modulate BMP signaling response in endothelial cells. Finally, we provide recent insight on how BMP signaling functions as a context dependent angiogenic cue.     

Measuring surface potential components necessary for transmembrane current computation using microfabricated arrays

This study was designed to test the feasibility of using microfabricated electrodes to record surface potentials with sufficiently fine spatial resolution to measure the potential gradients necessary for improved computation of transmembrane current density. To assess that feasibility, we recorded unipolar electrograms from perfused rabbit right ventricular free wall epicardium (n = 6) using electrode arrays that included 25-microm sensors fabricated onto a flexible substrate with 75-microm interelectrode spacing. Electrode spacing was therefore on the size scale of an individual myocyte. Signal conditioning adjacent to the sensors to control lead noise was achieved by routing traces from the electrodes to the back side of the substrate where buffer amplifiers were located. For comparison, recordings were also made using arrays built from chloridized silver wire electrodes of either 50-microm (fine wire) or 250-microm (coarse wire) diameters. Electrode separations were necessarily wider than with microfabricated arrays. Comparable signal-to-noise ratios (SNRs) of 21.2 +/- 2.2, 32.5 +/- 4.1, and 22.9 +/- 0.7 for electrograms recorded using microfabricated sensors (n = 78), fine wires (n = 78), and coarse wires (n = 78), respectively, were found. High SNRs were maintained in bipolar electrograms assembled using spatial combinations of the unipolar electrograms necessary for the potential gradient measurements and in second-difference electrograms assembled using spatial combinations of the bipolar electrograms necessary for surface Laplacian (SL) measurements. Simulations incorporating a bidomain representation of tissue structure and a two-dimensional network of guinea pig myocytes prescribed following the Luo and Rudy dynamic membrane equations were completed using 12.5-microm spatial resolution to assess contributions of electrode spacing to the potential gradient and SL measurements. In those simulations, increases in electrode separation from 12.5 to 75.0, 237.5, and 875.0 microm, which were separations comparable to the finest available with our microfabricated, fine wire, and coarse wire arrays, led to 10%, 42%, and 81% reductions in maximum potential gradients and 33%, 76%, and 96% reductions in peak-to-peak SLs. Maintenance of comparable SNRs for source electrograms was therefore important because microfabrication provides a highly attractive methods to achieve spatial resolutions necessary for improved computation of transmembrane current density.     

Fission yeast MO25 protein is localized at SPB and septum and is essential for cell morphogenesis

Cell morphogenesis is of fundamental significance in all eukaryotes for development, differentiation, and cell proliferation. In fission yeast, Drosophila Furry-like Mor2 plays an essential role in cell morphogenesis in concert with the NDR/Tricornered kinase Orb6. Mutations of these genes result in the loss of cell polarity. Here we show that the conserved proteins, MO25-like Pmo25, GC kinase Nak1, Mor2, and Orb6, constitute a morphogenesis network that is important for polarity control and cell separation. Intriguingly, Pmo25 was localized at the mitotic spindle pole bodies (SPBs) and then underwent translocation to the dividing medial region upon cytokinesis. Pmo25 formed a complex with Nak1 and was required for both the localization and kinase activity of Nak1. Pmo25 and Nak1 in turn were essential for Orb6 kinase activity. Further, the Pmo25 localization at the SPBs and the Nak1-Orb6 kinase activities during interphase were under the control of the Cdc7 and Sid1 kinases in the septation initiation network (SIN), suggesting a functional linkage between SIN and the network for cell morphogenesis/separation following cytokinesis.     

Potential nectin-1 binding site on herpes simplex virus glycoprotein d

Four glycoproteins (gD, gB, gH, and gL) are essential for herpes simplex virus (HSV) entry into cells. An early step of fusion requires gD to bind one of several receptors, such as nectin-1 or herpesvirus entry mediator (HVEM). We hypothesize that a conformational change in gD occurs upon receptor binding that triggers the other glycoproteins to mediate fusion. Comparison of the crystal structures of gD alone and gD bound to HVEM reveals that upon HVEM binding, the gD N terminus transitions from a flexible stretch of residues to a hairpin loop. To address the contribution of this transition to the ability of gD to trigger fusion, we attempted to "lock" the gD N terminus into a looped conformation by engineering a disulfide bond at its N and C termini. The resulting mutant (gD-A3C/Y38C) failed to trigger fusion in the absence of receptor, suggesting that formation of the loop is not the sole fusion trigger. Unexpectedly, although gD-A3C/Y38C bound HVEM, it failed to bind nectin-1. This was due to the key role played by Y38 in interacting with nectin-1. Since tyrosines are often "hot spot" residues at the center of protein-protein interfaces, we mutated residues that surround Y38 on the same face of gD and tested their binding and functional properties. Our results suggest that this region of gD is important for nectin-1 interaction and is distinct from but partially overlaps the site of HVEM binding. Unique gD mutants with altered receptor usage generated in this study may help dissect the roles played by various HSV receptors during infection.     

Investigation of factor Xa inhibitors containing non-amidine S1 elements

Several non-amidino S1 derivatives of the 1,2-diaminobenzene-based scaffold (4) were synthesized and evaluated for their ability to bind to the active site and inhibit the human protease factor Xa. A subset of these compounds were also evaluated for their anticoagulant effects in human plasma as measured by prothrombin time (PT).     

1-Pentyl-3-phenylacetylindoles, a new class of cannabimimetic indoles

A new class of cannabimimetic indoles, with 3-phenylacetyl or substituted 3-phenylacetyl substituents, has been prepared and their affinities for the cannabinoid CB1 and CB2 receptors have been determined. In general those compounds with a 2-substituted phenylacetyl group have good affinity for both receptors. The 4-substituted analogs have little affinity for either receptor, while the 3-substituted compounds are intermediate in their affinities. Two of these compounds, 1-pentyl-3-(2-methylphenylacetyl)indole (JWH-251) and 1-pentyl-3-(3-methoxyphenylacetyl)indole (JWH-302), have 5-fold selectivity for the CB1 receptor with modest affinity for the CB2 receptor. GTPgammaS determinations indicate that both compounds are highly efficacious agonists at the CB1 receptor and partial agonists at the CB2 receptor.