Dynamic Circadian Protein–Protein Interaction Networks Predict Temporal Organization of Cellular Functions

Essentially all biological processes depend on protein–protein interactions (PPIs). Timing of such interactions is crucial for regulatory function. Although circadian (∼24-hour) clocks constitute fundamental cellular timing mechanisms regulating important physiological processes, PPI dynamics on this timescale are largely unknown. Here, we identified 109 novel PPIs among circadian clock proteins via a yeast-two-hybrid approach. Among them, the interaction of protein phosphatase 1 and CLOCK/BMAL1 was found to result in BMAL1 destabilization. We constructed a dynamic circadian PPI network predicting the PPI timing using circadian expression data. Systematic circadian phenotyping (RNAi and overexpression) suggests a crucial role for components involved in dynamic interactions. Systems analysis of a global dynamic network in liver revealed that interacting proteins are expressed at similar times likely to restrict regulatory interactions to specific phases. Moreover, we predict that circadian PPIs dynamically connect many important cellular processes (signal transduction, cell cycle, etc.) contributing to temporal organization of cellular physiology in an unprecedented manner.     

Direct and indirect effects of elevated atmospheric CO2 on net ecosystem production in a Chesapeake Bay tidal wetland

The rapid increase in atmospheric CO₂ concentrations (C_a) has resulted in extensive research efforts to understand its impact on terrestrial ecosystems, especially carbon balance. Despite these efforts, there are relatively few data comparing net ecosystem exchange of CO₂ between the atmosphere and the biosphere (NEE), under both ambient and elevated C_a. Here we report data on annual sums of CO₂ (NEE_net) for 19 years on a Chesapeake Bay tidal wetland for Scirpus olneyi (C₃ photosynthetic pathway)‐ and Spartina patens (C₄ photosynthetic pathway)‐dominated high marsh communities exposed to ambient and elevated C_a (ambient + 340 ppm). Our objectives were to (i) quantify effects of elevated C_a on seasonally integrated CO₂ assimilation (NEE_net = NEE_day + NEE_night, kg C m^?2 y^?1) for the two communities; and (ii) quantify effects of altered canopy N content on ecosystem photosynthesis and respiration. Across all years, NEE_net averaged 1.9 kg m^?2 y^?1 in ambient C_a and 2.5 kg m^?2 y^?1 in elevated C_a, for the C₃‐dominated community. Similarly, elevated C_a significantly (P < 0.01) increased carbon uptake in the C₄‐dominated community, as NEE_net averaged 1.5 kg m^?2 y^?1 in ambient C_a and 1.7 kg m^?2 y^?1 in elevated C_a. This resulted in an average CO₂ stimulation of 32% and 13% of seasonally integrated NEE_net for the C₃‐ and C₄‐dominated communities, respectively. Increased NEE_day was correlated with increased efficiencies of light and nitrogen use for net carbon assimilation under elevated C_a, while decreased NEE_night was associated with lower canopy nitrogen content. These results suggest that rising C_a may increase carbon assimilation in both C₃‐ and C₄‐dominated wetland communities. The challenge remains to identify the fate of the assimilated carbon.     

Quantitative Analysis of Membrane Protein Transport Across the Nuclear Pore Complex

Nuclear transport of the Saccharomyces cerevisiae membrane proteins Src1/Heh1 and Heh2 across the NPC is facilitated by a long intrinsically disordered linker between the nuclear localization signal (NLS) and the transmembrane domain. The import of reporter proteins derived from Heh2 is dependent on the FG‐Nups in the central channel, and the linker can position the transport factor‐bound NLS in the vicinity of the FG‐Nups in the central channel, while the transmembrane segment resides in the pore membrane. Here, we present a quantitative analysis of karyopherin‐mediated import and passive efflux of reporter proteins derived from Heh2, including data on the mobility of the reporter proteins in different membrane compartments. We show that membrane proteins with extralumenal domains up to 174 kDa, terminal to the linker and NLS, passively leak out of the nucleus via the NPC, albeit at a slow rate. We propose that also during passive efflux, the unfolded linker facilitates the passage of extralumenal domains through the central channel of the NPC .     

Whole-body arginine dimethylation is associated with all-cause mortality in adult renal transplant recipients

Amino Acids - Arginine residues in proteins can be singly or doubly methylated post-translationally. Proteolysis of arginine-methylated proteins provides monomethyl arginine, asymmetric...     

Glass-like characteristics of intracellular motion in human cells

The motion in the cytosol of microorganisms such as bacteria and yeast has been observed to undergo a dramatic slowing down upon cell energy depletion. These observations have been interpreted as the motion being “glassy,” but whether this notion is useful also for active, motor-protein-driven transport in eukaryotic cells is less clear. Here, we use fluorescence microscopy of beads in human (HeLa) cells to probe the motion of membrane-surrounded structures that are carried along the cytoskeleton by motor proteins. Evaluating several hallmarks of glassy dynamics, we show that at short length scales, the motion is heterogeneous, is nonergodic, is well described by a model for the displacement distribution in glassy systems, and exhibits a decoupling of the exchange and persistence times. Overall, these results suggest that the short length scale behavior of objects that can be transported actively by motor proteins in human cells shares features with the motion in glassy systems.     

Ecological interactions between invasive and native fouling species in the reservoir of a hydroelectric plant

In this study, we investigate the main ecological interactions between fouling aquatic organisms (both invasive and native) present in the reservoir of the Governador José Richa hydroelectric plant, located in southern Brazil, and to identify the most suitable period for the interruption of machinery operation for cleaning and maintenance of the hydraulic systems of this plant. A total of 32 experimental plates were fixed to a metallic structure positioned close to the plant's water intake. Three species of invasive fouling were identified in our samples (Limnoperna fortunei [Mollusca], Cordylophora sp., and Hydra sp. [Cnidaria]) and six native taxa belonging to the phyla Protozoa, Ciliophora, Amoebozoa, and Arthropoda. Spring and summer were the seasons with the highest fouling rates, as well as densities of fouling organisms. The highest levels of diversity were recorded during the colder seasons. Several interactions between the organisms were identified, such as mutualism, commensalism, competition, epibiosis, cannibalism, and predation. The data obtained suggest that, from the biological point of view, the most suitable period for machine shutdown destined for the removal of biological fouling in the hydraulic systems of the studied plant is between the end of spring and the beginning of summer.

     

An Assessment of Introductory Restoration Courses in the United States and Canada

A considerable number of institutions offer courses in restoration ecology and its application, ecological restoration. We quantified the scope and structure of introductory restoration courses at 67 post‐secondary institutions by reviewing institutional course catalogs and course syllabi. Most courses were available at Research‐level institutions. More than half of the courses were offered within departments that focused on natural resource management, and were required or optional in a degree program. Most courses were taught in classroom settings during the academic year and were geared toward advanced students. Course titles suggested an emphasis on the science of restoration ecology over the practice of ecological restoration, and learning objectives focused primarily on concepts and less on skills and attitudes. Assessment was largely via conventional methods, notably exams. Many courses assigned readings from the primary literature; there was little consensus in terms of text selection. We conclude that restoration is being presented to students as an advanced undertaking and in largely theoretical terms. Although we were unable to consider other important elements such as thematic content, class size, or pedagogical method, our study provides a baseline assessment of introductory restoration courses that can be used to evaluate changes in restoration education or opportunities for restoration education in other countries. These results can inform the development of new introductory restoration courses, and raise important considerations in light of the development of a Practitioners' Certification Program by the Society for Ecological Restoration.