Contrast-FEL—A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches

A number of evolutionary hypotheses can be tested by comparing selective pressures among sets of branches in a phylogenetic tree. When the question of interest is to identify specific sites within genes that may be evolving differently, a common approach is to perform separate analyses on subsets of sequences and compare parameter estimates in a post hoc fashion. This approach is statistically suboptimal and not always applicable. Here, we develop a simple extension of a popular fixed effects likelihood method in the context of codon-based evolutionary phylogenetic maximum likelihood testing, Contrast-FEL. It is suitable for identifying individual alignment sites where any among the K≥2 sets of branches in a phylogenetic tree have detectably different ω ratios, indicative of different selective regimes. Using extensive simulations, we show that Contrast-FEL delivers good power, exceeding 90% for sufficiently large differences, while maintaining tight control over false positive rates, when the model is correctly specified. We conclude by applying Contrast-FEL to data from five previously published studies spanning a diverse range of organisms and focusing on different evolutionary questions.     

Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1

Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of the 3′ acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splicing enhancer (ESE3). Because HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge, and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate that the UP1 domain of heterogeneous nuclear ribonucleoprotein A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA-binding protein.     

β-Amyloid (Aβ) Oligomers Impair Brain-derived Neurotrophic Factor Retrograde Trafficking by Down-regulating Ubiquitin C-terminal Hydrolase,UCH-L1

We previously found that BDNF-dependent retrograde trafficking is impaired in AD transgenic mouse neurons. Utilizing a novel microfluidic culture chamber, we demonstrate that Aβ oligomers compromise BDNF-mediated retrograde transport by impairing endosomal vesicle velocities, resulting in impaired downstream signaling driven by BDNF/TrkB, including ERK5 activation, and CREB-dependent gene regulation. Our data suggest that a key mechanism mediating the deficit involves ubiquitin C-terminal hydrolase L1 (UCH-L1), a deubiquitinating enzyme that functions to regulate cellular ubiquitin. Aβ-induced deficits in BDNF trafficking and signaling are mimicked by LDN (an inhibitor of UCH-L1) and can be reversed by increasing cellular UCH-L1 levels, demonstrated here using a transducible TAT-UCH-L1 strategy. Finally, our data reveal that UCH-L1 mRNA levels are decreased in the hippocampi of AD brains. Taken together, our data implicate that UCH-L1 is important for regulating neurotrophin receptor sorting to signaling endosomes and supporting retrograde transport. Further, our results support the idea that in AD, Aβ may down-regulate UCH-L1 in the AD brain, which in turn impairs BDNF/TrkB-mediated retrograde signaling, compromising synaptic plasticity and neuronal survival.     

Transglutaminase and the Neuronal Cytoskeleton in Alzheimer''s Disease

Transglutaminase [EC 2.3.2.13, (R)-glutaminyl-peptide:amine gamma-glutamyltransferase], an enzyme that catalyzes the introduction of glutamine-lysine cross-links into proteins, was purified. Neurofilament and microtubule proteins were substrates for this enzyme but the insoluble neurofibrillary tangles (NFT) isolated from Alzheimer's disease brain were not substrates. In vitro cross-linking of neurofilaments and microtubules by the enzyme did not produce paired helical filaments (PHF), which are the major ultrastructural component of NFT. These results make it unlikely that PHF are formed by the straightforward cross-linking of neurofilaments or microtubules.     

Specific lysis of GABAergic synaptosomes by an antiserum to glutamate decarboxylase

An antiserum to pure glutamate decarboxylase (GAD) when incubated with rat cortical synaptosomes in the presence of complement caused release of 33-53% of lactate dehydrogenase (LDH) and 22-41% of total GAD. In addition most of the gamma-aminobutyrate (GABA) present was released. Anti-GAD antiserum alone, or complement alone, were without action. The antiserum plus complement had no effect on noradrenaline or choline uptake, and did not release choline acetylase (ChAT). Anti-ChAT serum plus complement released 30-37% of ChAT and 10-13% of LDH. It prevented choline uptake. This serum did not produce GAD release or prevent GABA, choline or noradrenaline uptake. When cortical synaptosomes were exposed to both antisera plus complement, their actions were strictly additive. The data indicate specific lysis of GABAergic and cholinergic synaptosomal sub-populations.     

Lipopolysaccharides from Pseudomonas maltophilia: composition of the lipopolysaccharide and structure of the side-chain polysaccharide from strain N.C.I.B. 9204

Lipopolysaccharide was extracted from defatted cell-walls of Pseudomonas maltophilia N.C.I.B. 9204. The major fatty acid components were 9-methyldecanoic acid, 2-hydroxy-9-methyldecanoic acid, 3-hydroxy-9-methyldecanoic acid, 3-hydroxy-dodecanoic acid, and 3-hydroxy-11-methyldodecanoic acid. Monosaccharide components of the phosphorylated core-oligosaccharide were D-glucose, D-mannose, D-galacturonic acid, 2-amino-2-deoxyglucose, and a 3-deoxyoctulosonic acid. The putative O-specific polysaccharide was composed mainly of 2-amino-2-deoxy-D-glucose, D-arabinose, and 6-deoxy-L-talose, but also contained an O-acetyl group and small proportions of rhamnose and 6-deoxy-3-O-methyltalose. Degradative and n.m.r. (1H and 13C) studies showed that the polymer had a branched trisaccharide repeating-unit with the following structure; the O-acetyl group was tentatively assigned to C-2 of the 6-deoxytalopyranosyl residue. (Formula: see text).     

Alzheimer's disease-like phosphorylation of the microtubule-associated protein tau by glycogen synthase kinase-3 in transfected mammalian cells

Background: Paired helical filaments (PHFs) are a characteristic pathological feature of Alzheimer's disease; their principal component is the microtubule-associated protein tau. The tau in PHFs (PHF-tau) is hyperphosphorylated, but the cellular mechanisms responsible for this hyperphosphorylation have yet to be elucidated. A number of kinases, including mitogen-activated protein (MAP) kinase, glycogen synthase kinase (GSK)-3α, GSK-3β and cyclin-dependent kinase-5, phosphorylate recombinant tau in vitro so that it resembles PHF-tau as judged by its reactivity with a panel of antibodies capable of discriminating between normal tau and PHF-tau, and by a reduced electrophoretic mobility that is characteristic of PHF-tau. To determine whether MAP kinase, GSK-3α and GSK-3β can also induce Alzheimer's disease-like phosphorylation of tau in mammalian cells, we studied the phosphorylation status of tau in primary neuronal cultures and transfected COS cells following changes in the activities of MAP kinase and GSK-3.Results Activating MAP kinase in cultures of primary neurons or transfected COS cells expressing tau isoforms did not increase the level of phosphorylation for any PHF-tau epitope investigated. But elevating GSK-3 activity in the COS cells by co-transfection with GSK-3α or GSK-3β decreased the electrophoretic mobility of tau so that it resembled that of PHF-tau, and induced reactivity with eight PHF-tau-selective monoclonal antibodies.Conclusion Our data indicate that GSK-3α and/or GSK-3β, but not MAP kinase, are good candidates for generating PHF-type phosphorylation of tau in Alzheimer's disease. The involvement of other kinases in the generation of PHFs cannot, however, be eliminated. Our results suggest that aberrant regulation of GSK-3 may be a pathogenic mechanism in Alzheimer's disease.     

Evidence for substrate guidance of primordial germ cells

Primordial germ cells (PGCs) have been removed from their normal migratory route in early embryos of Xenopus laevis, and their behaviour studied in vitro. They adhere to, and move over the upper surface of, layers of outgrowing cells from expiants of adult Xenopus mesentery. They move by the extrusion of single filopodia, elongation, forward streaming of the yolky cytoplasm and retraction of their trailing ends. When the underlying cells are polarized in one direction only, PGCs always elongate and move along the same direction. Furthermore, when PGCs elongate and move over less obviously polarized cells, they always do so in the direction of ‘stress fibres’ (actin bundles) in the underlying cells. A substrate-guidance hypothesis for PGC migration is only tenable if there is some orientation in their natural substrate in vivo. Using the scanning electron microscope, we demonstrate that the coelpmic lining cells, beneath which PGCs migrate up the dorsal mesentery of the gut, are orientated in the direction of travel. Furthermore, this orientation changes at the time of gonadal ridge formation. This raises the intriguing possibility that PGCs are guided for at least part of their migration in Xenopus laevis embryos by a substrate-guidance mechanism.