Estimation of the whole-plant CO2 compensation point of tobacco (Nicotiana tabacum L.)

The whole-plant CO₂ compensation point (Γ_plant) is the minimum atmospheric CO₂ level required for sustained growth. The minimum CO₂ requirement for growth is critical to understanding biosphere feedbacks on the carbon cycle during low CO₂ episodes; however, actual values of Γ_plant remain difficult to calculate. Here, we have estimated Γ_plant in tobacco by measuring the relative leaf expansion rate at several low levels of atmospheric CO₂, and then extrapolating the leaf growth vs. CO₂ response to estimate CO₂ levels where no growth occurs. Plants were grown under three temperature treatments, 19/15, 25/20 and 30/25°C day/night, and at CO₂ levels of 100, 150, 190 and 270 μmol CO₂ mol⁻¹ air. Biomass declined with growth CO₂ such that Γ_plant was estimated to be approximately 65 μmol mol⁻¹ for plants grown at 19/15 and 30/25°C. In the first 19 days after germination, plants grown at 100 μmol mol⁻¹ had low growth rates, such that most remained as tiny seedlings (canopy size <1 cm²). Most seedlings grown at 150 μmol mol⁻¹ and 30/25°C also failed to grow beyond the small seedling size by day 19. Plants in all other treatments grew beyond the small seedling size within 3 weeks of planting. Given sufficient time (16 weeks after planting) plants at 100 μmol mol⁻¹ eventually reached a robust size and produced an abundance of viable seed. Photosynthetic acclimation did not increase Rubisco content at low CO₂. Instead, Rubisco levels were unchanged except at the 100 and 150 μmol mol⁻¹ where they declined. Chlorophyll content and leaf weight per area declined in the same proportion as Rubisco, indicating that leaves became less expensive to produce. From these results, we conclude that the effects of very low CO₂ are most severe during seedling establishment, in large part because CO₂ deficiency slows the emergence and expansion of new leaves. Once sufficient leaf area is produced, plants enter the exponential growth phase and acquire sufficient carbon to complete their life cycle, even under warm conditions (30/25°C) and CO₂ levels as low as 100 μmol mol⁻¹.     

Both calmodulin and the unconventional myosin Myr4 regulate membrane trafficking along the recycling pathway of MDCK cells

In epithelial cells, endocytosed transferrin and its receptor, which cycle basolaterally, have been shown to transit through recycling endosomes which can also be accessed by markers internalized from the apical surface. In this work, we have used an in vitro assay to follow transfer of an endocytosed marker from apical or basolateral early endosomes to recycling endosomes labeled with transferrin. We show that calmodulin (CaM) function is necessary for transfer and identified myr4, a member of the unconventional myosin superfamily known to use CaM as a light chain, as a possible target protein for CaM. Since myr4 is believed to act as an actin-based mechanoenzyme, we tested the role of polymerized actin in the assay. Our data show that conditions which either prevent actin polymerization or induce the breakdown of existing filaments strongly inhibit interactions between recycling endosomes and either set of early endosomes. Altogether, our data indicate that trafficking at early steps of the endocytic pathway in Madin–Darby Canine Kidney cells depends on the actin-based mechanoenzyme myr4, its light chain CaM, and polymerized actin.     

Analysis of the mechanisms of Salmonella-induced actin assembly during invasion of host cells and intracellular replication

Salmonella enterica serovar Typhimurium (S. typhimurium) induces actin assembly both during invasion of host cells and during the course of intracellular bacterial replication. In this study, we investigated the involvement in these processes of host cell signalling pathways that are frequently utilized by bacterial pathogens to manipulate the eukaryotic actin cytoskeleton. We confirmed that Cdc42, Rac, and Arp3 are involved in S. typhimurium invasion of HeLa cells, and found that N-WASP and Scar/WAVE also play a role in this process. However, we found no evidence for the involvement of these proteins in actin assembly during intracellular replication. Cortactin was recruited by Salmonella during both invasion and intracellular replication. However, RNA interference directed against cortactin did not inhibit either invasion or intracellular actin assembly, although it resulted in increased cell spreading and a greater number of lamellipodia. We also found no role for either the GTPase dynamin or the formin family member mDia1 in actin assembly by intracellular bacteria. Collectively, these data provide evidence that signalling pathways leading to Arp2/3-dependent actin nucleation play an important role in S. typhimurium invasion, but are not involved in intracellular Salmonella-induced actin assembly, and suggest that actin assembly by intracellular S. typhimurium may proceed by a novel mechanism.     

KSHV‐TK is a tyrosine kinase that disrupts focal adhesions and induces Rho‐mediated cell contraction

Paradoxically, the thymidine kinase (TK) encoded by Kaposi sarcoma‐associated herpesvirus (KSHV) is an extremely inefficient nucleoside kinase, when compared to TKs from related herpesviruses. We now show that KSHV‐TK, in contrast to HSV1‐TK, associates with the actin cytoskeleton and induces extensive cell contraction followed by membrane blebbing. These dramatic changes in cell morphology depend on the auto‐phosphorylation of tyrosines 65, 85 and 120 in the N‐terminus of KSHV‐TK. Phosphorylation of tyrosines 65/85 and 120 results in an interaction with Crk family proteins and the p85 regulatory subunit of PI3‐Kinase, respectively. The interaction of Crk with KSHV‐TK leads to tyrosine phoshorylation of this cellular adaptor. Auto‐phosphorylation of KSHV‐TK also induces a loss of FAK and paxillin from focal adhesions, resulting in activation of RhoA‐ROCK signalling to myosin II and cell contraction. In the absence of FAK or paxillin, KSHV‐TK has no effect on focal adhesion integrity or cell morphology. Our observations demonstrate that by acting as a tyrosine kinase, KSHV‐TK modulates signalling and cell morphology.     

Connecting the Dots: How Connectedness to Multiple Contexts Influences the Psychological and Academic Adjustment of Urban Youth

Cluster analyses and hierarchical linear modeling were used to investigate the impact of perceptions of connectedness to family, school, and neighborhood contexts on academic and psycho-social outcomes for 437 urban ethnically diverse adolescents. Five profiles of connectedness to family, school, and neighborhood were identified. Two profiles were characterized by reports of either strong or weak connectedness to all contexts. The other three profiles were anchored by reports of low family connectedness, low neighborhood connectedness, or average connectedness. Race/ethnic differences were found in profiles and outcomes. Hierarchical linear models showed that each profile of connectedness was significantly associated with adolescents' self-report of grades, self-esteem, and depressive symptoms after adjusting for correlates, suggesting that the domain and number of contexts matter for positive youth development. These analyses underscore the importance of considering the independent and joint effects of family, schools, and neighborhoods on adolescent well-being. Implications for research and intervention are discussed.     

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

Background  

Computational analysis of metagenomes requires the taxonomical assignment of the genome contigs assembled from DNA reads of environmental samples. Because of the diverse nature of microbiomes, the length of the assemblies obtained can vary between a few hundred bp to a few hundred Kbp. Current taxonomic classification algorithms provide accurate classification for long contigs or for short fragments from organisms that have close relatives with annotated genomes. These are significant limitations for metagenome analysis because of the complexity of microbiomes and the paucity of existing annotated genomes.     

Kinesin-1-mediated capsid disassembly and disruption of the nuclear pore complex promote virus infection

Many viruses deliver their genomes into the host cell nucleus for replication. However, the size restrictions of the nuclear pore complex (NPC), which regulates the passage of proteins, nucleic acids, and solutes through the nuclear envelope, require virus capsid uncoating before viral DNA can access the nucleus. We report a microtubule motor kinesin-1-mediated and NPC-supported mechanism of adenovirus uncoating. The capsid binds to the NPC filament protein Nup214 and kinesin-1 light-chain Klc1/2. The nucleoporin Nup358, which is bound to Nup214/Nup88, interacts with the kinesin-1 heavy-chain Kif5c to indirectly link the capsid to the kinesin motor. Kinesin-1 disrupts capsids docked at Nup214, which compromises the NPC and dislocates nucleoporins and capsid fragments into the cytoplasm. NPC disruption increases nuclear envelope permeability as indicated by the nuclear influx of large cytoplasmic?dextran polymers. Thus, kinesin-1 uncoats viral DNA?and compromises NPC integrity, allowing viral genomes nuclear access to promote infection.