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.     

Distribution of indicator bacteria and Vibrio parahaemolyticus in sewage-polluted intertidal sediments

The impact of a sewage point source on the bacterial densities in an intertidal mud flat in Boston Harbor, Mass., was investigated. The area, Savin Hill Cove, acts as a receiving basin for a combined storm and sewage outlet (CSO). Preliminary examination of sediments and overlying water at high tide demonstrated that fecal coliforms were present in sediments at abundances 2 to 4 orders of magnitude higher than in the overlying water column. The following bacterial counts were determined from sediments along a sampling transect extending 460 m from the CSO: total bacteria by epifluorescent microscopy, heterotrophic bacteria by plate counts on nutrient-rich and nutrient-poor media, fecal coliforms and enterococci by membrane filtration, and Vibrio parahaemolyticus by a most-probable-number technique with a resuscitation step. Median sediment grain size, average tidal exposure, carbon/nitrogen ratio, and total organic carbon were also measured. All bacterial indices, except for V. parahaemolyticus, declined significantly with distance from the outfall. Multiple regression analysis indicated that tidal exposure (low tides) may affect densities of total bacteria. Fecal coliforms and enterococci were still present in appreciable numbers in sediments as far as 460 m away from the CSO. In contrast, V. parahaemolyticus densities did not correlate with the other bacterial counts nor with any of the environmental parameters examined. These results indicate that intertidal sediments which adjoin point sources of pollution are severely contaminated and should be considered as potentially hazardous reservoirs of sewage-borne diseases.     

Microtopography and the organization of two assemblages of coral reef fishes in the west indies

Two walls of Salt River Canyon, St. Croix, U.S. Virgin Islands are at the same depth in the fore reef environment and are separated by only 100 m, but they differ in microtopography. Replicate visual censuses of the fish assemblages on these two walls, by four saturation divers, gave consistent estimates of the species assemblages on the two walls. Significant faunal differences between the two walls are best understood in terms of combined features of coloration, predator avoidance, and feeding habit displayed regularly by individuals occupying a given microhabitat. It appears that characteristic sets of environmental circumstances occur within a habitat with sufficient frequency to give a consistent direction to natural selection, producing the patterns we have observed. Thus, form and function is predictable in relation to microhabitat, although species occurrence is not. The “order” and “chaos” concepts of community structure in coral reef fish, with their narrow focus on the predictability of species occurrence, underemphasize the possibility for a simple and direct role for natural selection in shaping the functional characteristics of an assemblage on a small scale     

Epidermal differentiation governs engineered skin biomechanics

Engineered skin must be mechanically strong to facilitate surgical application and prevent damage during the early stages of engraftment. However, the evolution of structural properties during culture, the relative contributions of the epidermis and dermis, and any correlation with tissue morphogenesis are not well known. These aspects are investigated by assessing the mechanical properties of engineered skin (ES) and engineered dermis (ED) during a 21-day culture period, including correlations with cellular metabolism, cellular organization and epidermal differentiation. During culture, the epidermis differentiates and begins to cornify, as evidenced by immunostaining and surface electrical capacitance. Tensile testing reveals that the ultimate tensile strength and linear stiffness increase linearly with time for ES, but are relatively unchanged for ED. ES strength correlates significantly with epidermal differentiation (p<0.001) and a composite strength model indicates that strength is largely determined by the epidermis. These data suggest that strategies to improve ES biomechanics should target the dermis. Additionally, time-dependant changes in average ES strength and percent elongation can be used to set upper bound limits on mechanical stimulation profiles to avoid tissue damage.     

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.     

Trends in tuna carbon isotopes suggest global changes in pelagic phytoplankton communities

Considerable uncertainty remains over how increasing atmospheric CO₂ and anthropogenic climate changes are affecting open‐ocean marine ecosystems from phytoplankton to top predators. Biological time series data are thus urgently needed for the world's oceans. Here, we use the carbon stable isotope composition of tuna to provide a first insight into the existence of global trends in complex ecosystem dynamics and changes in the oceanic carbon cycle. From 2000 to 2015, considerable declines in δ¹³C values of 0.8‰–2.5‰ were observed across three tuna species sampled globally, with more substantial changes in the Pacific Ocean compared to the Atlantic and Indian Oceans. Tuna recorded not only the Suess effect, that is, fossil fuel‐derived and isotopically light carbon being incorporated into marine ecosystems, but also recorded profound changes at the base of marine food webs. We suggest a global shift in phytoplankton community structure, for example, a reduction in ¹³C‐rich phytoplankton such as diatoms, and/or a change in phytoplankton physiology during this period, although this does not rule out other concomitant changes at higher levels in the food webs. Our study establishes tuna δ¹³C values as a candidate essential ocean variable to assess complex ecosystem responses to climate change at regional to global scales and over decadal timescales. Finally, this time series will be invaluable in calibrating and validating global earth system models to project changes in marine biota.     

Late‐life rapamycin treatment reverses age‐related heart dysfunction

Rapamycin has been shown to extend lifespan in numerous model organisms including mice, with the most dramatic longevity effects reported in females. However, little is known about the functional ramifications of this longevity‐enhancing paradigm in mammalian tissues. We treated 24‐month‐old female C57BL/6J mice with rapamycin for 3 months and determined health outcomes via a variety of noninvasive measures of cardiovascular, skeletal, and metabolic health for individual mice. We determined that while rapamycin has mild transient metabolic effects, there are significant benefits to late‐life cardiovascular function with a reversal or attenuation of age‐related changes in the heart. RNA‐seq analysis of cardiac tissue after treatment indicated inflammatory, metabolic, and antihypertrophic expression changes in cardiac tissue as potential mechanisms mediating the functional improvement. Rapamycin treatment also resulted in beneficial behavioral, skeletal, and motor changes in these mice compared with those fed a control diet. From these findings, we propose that late‐life rapamycin therapy not only extends the lifespan of mammals, but also confers functional benefits to a number of tissues and mechanistically implicates an improvement in contractile function and antihypertrophic signaling in the aged heart with a reduction in age‐related inflammation.