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.     

Ammonium and nitrate uptake by barley genotypes in diurnally fluctuating root temperatures simulating till and no-till conditions

The morphological development and N uptake patterns of spring barley (Hordeum vulgare L.) genotypes of Northern European (Nordic) and Pacific Northwest US (PNW) origin were compared under two diurnally fluctuating root temperature regimes in solution culture. The two regimes, 15/5°C and 9/5°C day maximum/night minimum temperatures, simulated soil temperature differences between tilled vs. heavy-residue, no-till conditions, respectively, observed during early spring in eastern Washington. Previous field experiments indicated that some of the Nordic genotypes accumulated more N and dry matter than the PNW cultivars during early spring under no-till conditions. The objective of this experiment was to determined whether these differences 1) are dependent on the temperature of the rooting environment, and 2) are correlated with genotypic differences in NH₄ ⁺ and NO₃ ^– uptake. Overall, shoot N and dry matter accumulation was reduced by 40% due to lower root temperatures during illumination. Leaf emergence was slowed by 14 to 22%, and tiller production was also inhibited. All genotypes absorbed more ammonium than nitrate from equimolar solutions, and the proportion of total N absorbed as NH₄ ⁺ was slightly higher in the 9/5°C than the 15/5°C regime. A Finnish genotype, HJA80201, accumulated significantly more shoot N than the PNW cultivars, Clark and Steptoe, and also more than a Swedish cultivar, Pernilla, in the 9/5°C regime. In the 15/5°C regime Steptoe did not differ in shoot N from the Nordic genotypes, while Clark remained significantly lower. These differences were not correlated to relative propensity for N form. Root lengths of the Nordic genotypes were significantly greater than the PNW genotypes grown under the 9/5°C regime, while the root lengths in the warmer root temperture regime were not significantly different among genotypes. Higher root elongation rates under low soil temperature conditions may be an inherent adaptive mechanism of the Nordic genotypes. Overall, the data indicate that lower maximum daytime temperatures of the soil surface layer likely account for a significant portion of the growth reductions and lower N uptake observed in no-till systems.     

The effect of sulfhydryl oxidation on the morphology of immature hamster epididymal spermatozoa induced to acquire motility in vitro

Immotile spermatozoa from the caput epididymidis become progressively motile when incubated in medium containing theophylline, seminal plasma, and albumin. We previously reported that under these incubation conditions the spermatozoa induced to acquire motility exhibited a marked flagellar angularity, with the sperm head or midpiece bent 90-180 degrees towards the tail. In addition, we demonstrated that sperm flagellar bending did not occur when the sulfhydryl oxidant diamide was added to the motility induction medium. In the present study, we examined further the effect of sulfhydryl oxidation on the morphology and sulfhydryl content of immature caput spermatozoa induced to acquire motility in vitro. We found that flagellar bending was prevented and sperm flagellar straightness was maintained in a dose-dependent manner by diamide. Moreover, flow cytometric analysis of caput sperm sulfhydryls using the sulfhydryl reagent monobromobimane (mBBr) revealed that 1) diamide oxidizes caput sperm sulfhydryls, and 2) less than 15% of the total reactive sperm sulfhydryls were oxidized at diamide concentrations capable of preventing sperm angulation. Sodium tetrathionate (NaTT), another sulfhydryl oxidant, and hamster cauda epididymal fluid (CEF) containing sulfhydryl oxidase enzyme activity also maintained flagellar straightness in induced caput spermatozoa and oxidized sperm sulfhydryls. The flagellar straightness in caput spermatozoa treated with sulfhydryl oxidants, however, was temporary; with extended incubation, diamide- or CEF-treated spermatozoa exhibited flagellar bending. Additional studies showed that the flagellar straightness observed in sulfhydryl-oxidized spermatozoa was sustained when nitrofurantoin, an inhibitor of glutathione reductase, was included in the induction medium. Flow cytometric analysis of nitrofurantoin-treated spermatozoa showed that nitrofurantoin maintained the sperm disulfides formed by diamide and prevented the reduction of sperm disulfides back to sulfhydryls. Taken together, these studies demonstrate the significance of sulfhydryl oxidation in maintaining the morphology of immature caput epididymal spermatozoa induced to acquire motility in vitro and suggest that sulfhydryl oxidation may be important in the development of motility during sperm epididymal maturation in vivo.     

Clinical Value of Teichoic Acid Antibody Titers in the Diagnosis and Management of the Staphylococcemias

Differentiation of endocarditic from nonendocarditic Staphylococcus aureus (SA) septicemia is prognostically and therapeutically important. A study of 68 cases of either SA or streptococcal sepsis, including 50 cases of SA sepsis of both cardiac and noncardiac origin, was done to determine the presence and titer of serum teichoic acid antibodies (TAA''s) by double immunodiffusion. Thirty-seven uninfected controls were also examined. There was no statistical difference in either incidence or peak TAA titers in endocardial versus deepseated, extracardiac SA sepsis. However, in both of these groups, incidence and peak titers were significantly higher than in intravascular catheter-related SA sepsis, streptococcal endocarditis and controls (P<0.05). Peak TAA titers in SA sepsis develop on admission or shortly thereafter (6 to 11 days) and permit early decisions on degree of tissue infection, likelihood of metastatic seeding and necessity for higher-dose, longer-term antibiotic therapy.Cases of catheter-related SA sepsis with no clinical evidence of metastatic SA seeding and with negative or low-titered (1:1) TAA''s were classified as superficial sepsis. Treatment consisted of short-term, low-dose antistaphylococcal regimens and catheter removal. In posttherapy follow-up after 6 to 12 weeks, all of the patients were cured and no signs of endocarditis or deepseated SA infection developed.     

Intraspecific host discrimination and larval competition inMicroplitis croceipes,Microplitis demolitor,Cotesia kazak (HYM.: Braconidae) andHyposoter didymator HYM: Ichneumonidae), parasitoids ofHeliothis virescens (LEP.: Noctuidae)

Intraspecific host discrimination and larval competition were studied forMicroplitis croceipes (Cresson),Microplitis demolitor Wilkinson,Cotesia kazak (Telenga), andHyposoter didymator (Thunberg), solitary endoparasitoids of the tobacco budworm,Heliothis virescens (F.). In ovipositional choice tests between unparasitized and parasitized hosts, the mean number of ovipositions for unparasitized hosts was significantly higher than the mean number of ovipositions for hosts parasitized once by a conspecific female forC. kazak andH. didymator, demonstrating that females of these two species discriminate against hosts recently (within a few seconds) parasitized by a conspecific female. No significant difference in oviposition occurred between these two kinds of hosts forM. croceipes andM. demolitor. Mean percent parasitization by a second conspecific female was determined at 24, 48, and 72 h delays in time between the first and second female attack, and with no delay. Except for the 0 h time delay forC. kazak andH. didymator, percent parasitization by a second conspecific female generally decreased as the delay in time between the first and second female attack increased. When the second parasitization immediately followed the first, one parasitoid larva always eliminated the other by physical combat. With a 24 or 48 h delay between the first and second parasitization, the younger larva was the victor over the older larva forM. croceipes, M. demolitor andC. kazak in at least 50% of the cases. Elimination of older larvae by younger larva was by physical attack. However, forH. didymator, the older instar was the victor, and elimination of younger larvae by older larvae was probably through physiological processes. Further, older larvae ofH. didymator apparently killed the eggs of the second female by physiological processes.      

Organization of enzymes of glycolysis and of glutathione metabolism in human red cell membranes.

1) The activities of 16 enzymes of glycolysis and of glutathione metabolism were determined in intact human red cell membranes (ghosts) which were prepared by hypotonic hemolysis. 2) Enzymes and hemoglobin of the ghosts were resolved by two toluene extractions. Only the four enzymes hexokinase, fructose-bisphosphate aldolase, glyceraldehyde-phosphate dehydrogenase and pyruvate kinase could not be released completely from the ghosts. 3) The residual membrane fraction, which was obtained after the toluene extraction of ghosts prepared at 30 imOsM, contained 0.02% of the original hemoglobin content of the red cell. Between 6.5 and 23% of the hemolysate activities of glyceraldehyde-phosphate dehydrogenase, phosphoglycerate kinase, pyruvate kinase and fructose-bisphosphate aldolase were detected in this fraction after mechanical disruption. 4) Sonication of intact ghosts increased the activities of fructose-bisphosphate aldolase, pyruvate kinase and phosphoglycerate kinase. 5) In "white" ghosts prepared at 5 imOsM phosphate buffer which contained 0.5% of the original hemoglobin the activities of fructose-bisphosphate aldolase and glyceraldehyde-phosphate dehydrogenase were detected at high levels. The activities of pyruvate kinase and phosphoglycerate kinase were low in these preparations. 6) The results indicate that one part of all enzymes is loosely attached to the inner surface of the membrane as is hemoglobin. A second part, the "cryptic enzyme activity", is available after resolving by toluene. A residual part of four enzymes is firmly bound to the membrane. Two of them (fructose-bisphosphate aldolase and glyceraldehyde-phosphate dehydrogenase) are oriented toward the inner surface of the membrane, whereas pyruvate kinase and phosphoglycerate kinase are hidden in the lipid core of the membrane.     

Vesicular trafficking permits evasion of cGAS/STING surveillance during initial human papillomavirus infection

Oncogenic human papillomaviruses (HPVs) replicate in differentiating epithelium, causing 5% of cancers worldwide. Like most other DNA viruses, HPV infection initiates after trafficking viral genome (vDNA) to host cell nuclei. Cells possess innate surveillance pathways to detect microbial components or physiological stresses often associated with microbial infections. One of these pathways, cGAS/STING, induces IRF3-dependent antiviral interferon (IFN) responses upon detection of cytosolic DNA. Virion-associated vDNA can activate cGAS/STING during initial viral entry and uncoating/trafficking, and thus cGAS/STING is an obstacle to many DNA viruses. HPV has a unique vesicular trafficking pathway compared to many other DNA viruses. As the capsid uncoats within acidic endosomal compartments, minor capsid protein L2 protrudes across vesicular membranes to facilitate transport of vDNA to the Golgi. L2/vDNA resides within the Golgi lumen until G2/M, whereupon vesicular L2/vDNA traffics along spindle microtubules, tethering to chromosomes to access daughter cell nuclei. L2/vDNA-containing vesicles likely remain intact until G1, following nuclear envelope reformation. We hypothesize that this unique vesicular trafficking protects HPV from cGAS/STING surveillance. Here, we investigate cGAS/STING responses to HPV infection. DNA transfection resulted in acute cGAS/STING activation and downstream IFN responses. In contrast, HPV infection elicited minimal cGAS/STING and IFN responses. To determine the role of vesicular trafficking in cGAS/STING evasion, we forced premature viral penetration of vesicular membranes with membrane-perturbing cationic lipids. Such treatment renders a non-infectious trafficking-defective mutant HPV infectious, yet susceptible to cGAS/STING detection. Overall, HPV evades cGAS/STING by its unique subcellular trafficking, a property that may contribute to establishment of infection.