Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides (Figure 1). The growing product double-strand DNA (dsDNA) is extended with laminar flow and visualized by using an intercalating dye. Measuring the position of the growing DNA end in real time allows precise determination of replication rate (Figure 2). Furthermore, the length of completed DNA products reports on the processivity of replication. This experiment can be performed very easily and rapidly and requires only a fluorescence microscope with a reasonably sensitive camera.     

Genome‐wide association study of word reading: Overlap with risk genes for neurodevelopmental disorders

Reading disabilities (RD) are the most common neurocognitive disorder, affecting 5% to 17% of children in North America. These children often have comorbid neurodevelopmental/psychiatric disorders, such as attention deficit/hyperactivity disorder (ADHD). The genetics of RD and their overlap with other disorders is incompletely understood. To contribute to this, we performed a genome‐wide association study (GWAS) for word reading. Then, using summary statistics from neurodevelopmental/psychiatric disorders, we computed polygenic risk scores (PRS) and used them to predict reading ability in our samples. This enabled us to test the shared aetiology between RD and other disorders. The GWAS consisted of 5.3 million single nucleotide polymorphisms (SNPs) and two samples; a family‐based sample recruited for reading difficulties in Toronto (n = 624) and a population‐based sample recruited in Philadelphia [Philadelphia Neurodevelopmental Cohort (PNC)] (n = 4430). The Toronto sample SNP‐based analysis identified suggestive SNPs (P ~ 5 × 10^?7) in the ARHGAP23 gene, which is implicated in neuronal migration/axon pathfinding. The PNC gene‐based analysis identified significant associations (P < 2.72 × 10^?6) for LINC00935 and CCNT1, located in the region of the KANSL2/CCNT1/LINC00935/SNORA2B/SNORA34/MIR4701/ADCY6 genes on chromosome 12q, with near significant SNP‐based analysis. PRS identified significant overlap between word reading and intelligence (R² = 0.18, P = 7.25 × 10^?181), word reading and educational attainment (R² = 0.07, P = 4.91 × 10^?48) and word reading and ADHD (R² = 0.02, P = 8.70 × 10^?6; threshold for significance = 7.14 × 10^?3). Overlap was also found between RD and autism spectrum disorder (ASD) as top‐ranked genes were previously implicated in autism by rare and copy number variant analyses. These findings support shared risk between word reading, cognitive measures, educational outcomes and neurodevelopmental disorders, including ASD.     

Dominant drivers of plant community assembly vary by soil type and time in reclaimed forests

Information on plant community assembly mechanisms is limited on forest reclamation sites after mining in the Canadian boreal forest. We assessed the change in plant community composition after Year 2 and Year 5 on species-rich forest floor mineral mix (FFMM) and species-poor peat mineral mix (PMM) reclamation soils by examining assembly mechanisms, i.e., seed bank, seed rain, biotic dispersal, vegetative expansion, and competition. Initial plant cover and diversity were greater on FFMM due to non-native species originating from the seed bank, which had 5× more seeds in the FFMM. By Year 5, both soil types had approximately 40% cover and 80 species richness due to the addition of wind and biotic-dispersed species and were characterized by a shift towards native species. Native forbs using vegetative reproduction expanded up to 2 m from FFMM into PMM. At Year 5 competition does not seem to have a large role in the structuring of the vegetation community. Overall, multiple factors were involved in structuring plant communities on reclamation sites, but we observed a general convergence between plant communities on different soil types in a relatively short period of time.

     

Investigation of the Molecular Nature of Low-molecular-mass Cobalt(II) Ions in Isolated Osteoarthritic Knee-joint Synovial Fluid

High field ¹H NMR spectroscopy demonstrated that addition of Co(II) ions to osteoarthritic knee-joint synovial fluid (SF) resulted in its complexation by a range of biomolecules, the relative efficacies of these complexants/chelators being citrate ? histidine ～ threonine?glycine ～ glutamate ～ glutamine ～ phenylalanine ～ tyrosine > formate > lactate?alanine > valine > acetate > pyruvate > creatinine, this order reflecting the ability of these ligands to compete for the available Co(II) in terms of (1) thermodynamic equilibrium constants for the formation of their complexes and (2) their SF concentrations. Since many of these SF Co(II) complexants (e.g. histidinate) serve as powerful ^?OH scavengers, the results acquired indicate that any of this radical generated from the Co(II) source in such complexes via Fenton or pseudo-Fenton reaction systems will be “site-specifically” scavenged. The significance of these observations with regard to cobalt toxicity and the in vivo corrosion of cobalt-containing metal alloy joint prostheses (e.g. CoCr alloys) is discussed.     

The impact of two non-native plant species on native flora performance: potential implications for habitat restoration

Both Impatiens glandulifera and Fallopia japonica are highly invasive plant species that have detrimental impacts on native biodiversity in areas where they invade and form dense monocultures. Both species are weakly dependent on arbuscular mycorrhizal fungi (AMF) for their growth and, therefore, under monotypic stands, the AMF network can become depauperate. We evaluated the impact of I. glandulifera and F. japonica on the performance (expressed as shoot biomass) of three UK native species (Plantago lanceolata, Lotus corniculatus and Trifolium pratense) grown in soil collected from under stands of both invasive plants and compared to plants grown in soil from under stands of the corresponding native vegetation. All native species had a higher percentage colonisation of AMF when grown in uninvaded soil compared to the corresponding invaded soil. P. lanceolata and L. corniculatus had a higher biomass when grown in uninvaded soil compared to corresponding invaded soil indicating an indirect impact from the non-native species. However, for T. pratense there was no difference in biomass between soil types related to I. glandulifera, suggesting that the species is more reliant on rhizobial bacteria. We conclude that simply managing invasive populations of non-native species that are weakly, or non-dependent, on AMF is inadequate for habitat restoration as native plant colonisation and establishment may be hindered by the depleted levels of AMF in the soil below invaded monocultures. We suggest that the reintroduction of native plants to promote AMF proliferation should be incorporated into future management plans for habitats degraded by non-native plant species.     

Genetic Background Can Result in a Marked or Minimal Effect of Gene Knockout (GPR55 and CB2 Receptor) in Experimental Autoimmune Encephalomyelitis Models of Multiple Sclerosis

Endocannabinoids and some phytocannabinoids bind to CB₁ and CB₂ cannabinoid receptors, transient receptor potential vanilloid one (TRPV1) receptor and the orphan G protein receptor fifty-five (GPR55). Studies using C57BL/10 and C57BL/6 (Cnr2 ^tm1Zim) CB₂ cannabinoid receptor knockout mice have demonstrated an immune-augmenting effect in experimental autoimmune encephalomyelitis (EAE) models of multiple sclerosis. However, other EAE studies in Biozzi ABH mice often failed to show any treatment effect of either CB₂ receptor agonism or antagonism on inhibition of T cell autoimmunity. The influence of genetic background on the induction of EAE in endocannabinoid system-related gene knockout mice was examined. It was found that C57BL/6.GPR55 knockout mice developed less severe disease, notably in female mice, following active induction with myelin oligodendrocyte glycoprotein 35-55 peptide. In contrast C57BL/6.CB₂ (Cnr2 ^Dgen) receptor knockout mice developed augmented severity of disease consistent with the genetically and pharmacologically-distinct, Cnr2 ^tm1Zim mice. However, when the knockout gene was bred into the ABH mouse background and EAE induced with spinal cord autoantigens the immune-enhancing effect of CB₂ receptor deletion was lost. Likewise CB₁ receptor and transient receptor potential vanilloid one knockout mice on the ABH background demonstrated no alteration in immune-susceptibility, in terms of disease incidence and severity of EAE, in contrast to that reported in some C57BL/6 mouse studies. Furthermore the immune-modulating influence of GPR55 was marginal on the ABH mouse background. Whilst sedative doses of tetrahydrocannabinol could induce immunosuppression, this was associated with a CB₁ receptor rather than a CB₂ receptor-mediated effect. These data support the fact that non-psychoactive doses of medicinal cannabis have a marginal influence on the immune response in MS. Importantly, it adds a note of caution for the translational value of some transgenic/gene knockout and other studies on low-EAE susceptibility backgrounds with inconsistent disease course and susceptibility.