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.     

Does vitellogenin inhibit lipoprotein lipase in the laying hen?

Vitellogenin isolated from laying-hen plasma strongly inhibited chicken adipose-tissue lipoprotein lipase in vitro, but inhibition was reduced or prevented by Ca2+ and Mg2+ ions and by partial dephosphorylation. Plasma from blood collected from laying hens using EDTA as anticoagulant was a potent inhibitor of lipoprotein lipase, but serum from laying hen blood caused inhibition only when dilute or after addition of EDTA. Heparin reduced or abolished the inhibition of lipoprotein lipase by plasma, serum and purified vitellogenin. The results suggest that inhibition of lipoprotein lipase by vitellogenin requires the presence of charged phosphate groups on vitellogenin and an unoccupied heparin-binding site on the enzyme. Neither condition is likely to occur in the laying hen in vivo.     

Application of a bioinformatics training delivery method for reaching dispersed and distant trainees

Many initiatives have addressed the global need to upskill biologists in bioinformatics tools and techniques. Australia is not unique in its requirement for such training, but due to its large size and relatively small and geographically dispersed population, Australia faces specific challenges. A combined training approach was implemented by the authors to overcome these challenges. The “hybrid” method combines guidance from experienced trainers with the benefits of both webinar-style delivery and concurrent face-to-face hands-on practical exercises in classrooms. Since 2017, the hybrid method has been used to conduct 9 hands-on bioinformatics training sessions at international scale in which over 800 researchers have been trained in diverse topics on a range of software platforms. The method has become a key tool to ensure scalable and more equitable delivery of short-course bioinformatics training across Australia and can be easily adapted to other locations, topics, or settings.     

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.     

Metabolic cost of generating muscular force in human walking: insights from load-carrying and speed experiments.

We sought to understand how leg muscle function determines the metabolic cost of walking. We first indirectly assessed the metabolic cost of swinging the legs and then examined the cost of generating muscular force during the stance phase. Four men and four women walked at 0.5, 1.0, 1.5, and 2.0 m/s carrying loads equal to 0, 10, 20, and 30% body mass positioned symmetrically about the waist. The net metabolic rate increased in nearly direct proportion to the external mechanical power during moderate-speed (0.5-1.5 m/s) load carrying, suggesting that the cost of swinging the legs is relatively small. The active muscle volume required to generate force on the ground and the rate of generating this force accounted for >85% of the increase in net metabolic rate across moderate speeds and most loading conditions. Although these factors explained less of the increase in metabolic rate between 1.5 and 2.0 m/s ( approximately 50%), the cost of generating force per unit volume of active muscle [i.e., the cost coefficient (k)] was similar across all conditions [k = 0.11 +/- 0.03 (SD) J/cm3]. These data indicate that, regardless of the work muscles do, the metabolic cost of walking can be largely explained by the cost of generating muscular force during the stance phase.     

Autoactivation of human plasma prekallikrein

Incubation of purified human plasma prekallikrein with sulfatides or dextran sulfate resulted in spontaneous activation of prekallikrein as judged by the appearance of amidolytic activity toward the chromogenic substrate H-D-Pro-Phe-Arg-p-nitroanilide. The time course of generation of amidolytic activity was sigmoidal with an apparent lag phase that was followed by a relatively rapid activation until finally a plateau was reached. Soybean trypsin inhibitor completely blocked prekallikrein activation whereas corn, lima bean, and ovomucoid trypsin inhibitors did not. The Ki of the reversible inhibitor benzamidine for autoactivation (240 microM) was identical to the Ki of benzamidine for kallikrein. Thus, spontaneous prekallikrein activation and kallikrein showed the same specificity for a number of serine protease inhibitors. This indicates that prekallikrein is activated by its own enzymatically active form, kallikrein. Immunoblotting analysis of the time course of activation showed that, concomitant with the appearance of amidolytic activity, prekallikrein was cleaved. However, prekallikrein was not quantitatively converted into two-chain kallikrein since other polypeptide products were visible on the gels. This accounts for the observation that in amidolytic assays not all prekallikrein present in the reaction mixture was measured as active kallikrein. Kinetic analysis showed that prekallikrein activation can be described by a second-order reaction mechanism in which prekallikrein is activated by kallikrein. The apparent second-order rate constant was 2.7 X 10(4) M-1 s-1 (pH 7.2, 50 microM sulfatides, ionic strength I = 0.06, at 37 degrees C). Autocatalytic prekallikrein activation was strongly dependent on the ionic strength, since there was a considerable decrease in the second-order rate constant of the reaction at high salt concentrations. In support of the autoactivation mechanism it was found that increasing the amount of kallikrein initially present in the reaction mixture resulted in a significant reduction of the lag period and a rapid completion of the reaction while the second-order rate constant was not influenced. Our data support a prekallikrein autoactivation mechanism in which surface-bound kallikrein activates surface-bound prekallikrein.