Real-time monitoring of subcellular H2O2 distribution in Chlamydomonas reinhardtii

Hydrogen peroxide (H₂O₂) is recognized as an important signaling molecule in plants. We sought to establish a genetically encoded, fluorescent H₂O₂ sensor that allows H₂O₂ monitoring in all major subcompartments of a Chlamydomonas cell. To this end, we used the Chlamydomonas Modular Cloning toolbox to target the hypersensitive H₂O₂ sensor reduction–oxidation sensitive green fluorescent protein2-Tsa2ΔC_R to the cytosol, nucleus, mitochondrial matrix, chloroplast stroma, thylakoid lumen, and endoplasmic reticulum (ER). The sensor was functional in all compartments, except for the ER where it was fully oxidized. Employing our novel sensors, we show that H₂O₂ produced by photosynthetic linear electron transport (PET) in the stroma leaks into the cytosol but only reaches other subcellular compartments if produced under nonphysiological conditions. Furthermore, in heat-stressed cells, we show that cytosolic H₂O₂ levels closely mirror temperature up- and downshifts and are independent from PET. Heat stress led to similar up- and downshifts of H₂O₂ levels in the nucleus and, more mildly, in mitochondria but not in the chloroplast. Our results thus suggest the establishment of steep intracellular H₂O₂ gradients under normal physiological conditions with limited diffusion into other compartments. We anticipate that these sensors will greatly facilitate future investigations of H₂O₂ biology in plant cells.

The establishment of a hypersensitive H₂O₂ sensor in six major compartments of the Chlamydomonas cell reveals steep intracellular H₂O₂ gradients under normal physiological conditions with limited diffusion into other compartments.     

Human DIMT1 generates N26,6A-dimethylation–containing small RNAs

Dimethyladenosine transferase 1 (DIMT1) is an evolutionarily conserved RNA N^6,6-dimethyladenosine (m₂^6,6A) methyltransferase. DIMT1 plays an important role in ribosome biogenesis, and the catalytic activity of DIMT1 is indispensable for cell viability and protein synthesis. A few RNA-modifying enzymes can install the same modification in multiple RNA species. However, whether DIMT1 can work on RNA species other than 18S rRNA is unclear. Here, we describe that DIMT1 generates m₂^6,6A not only in 18S rRNA but also in small RNAs. In addition, m₂^6,6A in small RNAs were significantly decreased in cells expressing catalytically inactive DIMT1 variants (E85A or NLPY variants) compared with cells expressing wildtype DIMT1. Both E85A and NLPY DIMT1 variant cells present decreased protein synthesis and cell viability. Furthermore, we observed that DIMT1 is highly expressed in human cancers, including acute myeloid leukemia. Our data suggest that downregulation of DIMT1 in acute myeloid leukemia cells leads to a decreased m₂^6,6A level in small RNAs. Together, these data suggest that DIMT1 not only installs m₂^6,6A in 18S rRNA but also generates m₂^6,6A-containing small RNAs, both of which potentially contribute to the impact of DIMT1 on cell viability and gene expression.     

A Comparative Study of Leaf Breakdown of Three Native Tree Species in a Slowly‐Flowing Headwater Stream in the Colombian Andes

The dynamics of leaf breakdown in a headwater Colombian stream were evaluated for the native tree species Myrsine guianensis, Cupania latifolia and Nectandra lineatifolia using coarse and fine mesh litter bags. Ten bags of each species (five of each mesh size) were retrieved from the stream at 1, 8, 15, 30, 60 and 120 days. k values ranged from 0.0008 to 0.0058 day^–1 and density of macroinvertebrates from 35 to 55 individuals per leaf bag, peaking at day 8. Myrsine guianensis degraded more rapidly than the other species for both coarse and fine mesh bags. This species and Nectandra lineatifolia presented differences in k values between coarse and fine mesh bags, suggesting that macroinvertebrates influenced the decay rate. Despite the low densities of macroinvertebrates found, shredders represented 12.7% of individuals and 50 to 68% of the invertebrate biomass in bags, indicating that this functional feeding group was an important component of fauna associated with litter breakdown in this first order tropical stream. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Initial studies with high resolution TEM and electron energy loss spectroscopy studies of ferritin cores extracted from brains of patients with progressive supranuclear palsy and Alzheimer disease.

Studies of crystallographic structure and composition of core nanocrystals of ferritin bound to aberrant tau filaments extracted from progressive supranuclear Palsy (PSP) and Alzheimer disease (AD) brain tissues were performed using high resolution transmission electron microscopy (HRTEM) and electron energy loss spectroscopy (EELS). The results were compared with those obtained from synthetic Fe3O4 crystal (magnetite) and horse spleen ferritin cores. Core dimensions of ferritin molecules from PSP and AD were similar to those found in normal brain. Ferritin cores nanocrystals in AD seems to have less ordered structure than in PSP. Some nanocrystals did not have the hexagonal ferrihydrite structure generally found in healthy ferritin but rather a cubic structure similar to magnetite, a crystalline form in which both Fe2+ and Fe3+ are present. The presence of ferrous ion, Fe2+, may indicate some dysfunction in these pathological ferritins that might contribute to production of free radicals via the Fenton reaction involved in neurodegeneration.     

Soil‐mediated effects on germination and seedling growth of coastal wattle (Acacia sophorae) by the environmental weed,bitou bush (Chrysanthemoides monilifera ssp. rotundata)

Bitou bush (Chrysanthemoides monilifera ssp. rotundata; Asteraceae) is a major woody weed that competes with the native legume Acacia sophorae in coastal ecosystems of eastern Australia. Three glasshouse experiments examined whether litter or soil from beneath bitou bush or Acacia plants could influence seed germination and seedling growth of A. sophorae. The presence of litter decreased seed germinability and this effect was greater for bitou bush litter than for Acacia litter. Shoot growth was increased by the addition of Rhizobium after 40 days, irrespective of soil type. After 78 days, shoot and root biomass were significantly lower for seedlings grown in bitou bush soil than for those grown in Acacia soil. There was a non‐significant trend towards a lower median population of Rhizobium in the soil beneath bitou bush than in that beneath Acacia. The results demonstrated a slight effect of bitou bush on the growth of A. sophorae, which could, however, be overshadowed by the judicious use of herbicides or fire for weed control and revegetation.     

Debate: A subversive view of subsets - a dissident clinician's opinion

Clinical trialists and statisticians are very wary of subgroup analysis, for good reasons. Clinicians have to deal with situations in which subgroups of patients differ widely from one another in their prognosis and response to treatment. Few trials are large enough to demonstrate convincingly these differences in outcome, but often provide suggestive evidence. Should we ignore this and treat all patients as the same, or should we allow dubious statistical evidence to buttress biological plausibility in making clinical decisions?     

Geographic differences in genetic susceptibility to IgA nephropathy: GWAS replication study and geospatial risk analysis

IgA nephropathy (IgAN), major cause of kidney failure worldwide, is common in Asians, moderately prevalent in Europeans, and rare in Africans. It is not known if these differences represent variation in genes, environment, or ascertainment. In a recent GWAS, we localized five IgAN susceptibility loci on Chr.6p21 (HLA-DQB1/DRB1, PSMB9/TAP1, and DPA1/DPB2 loci), Chr.1q32 (CFHR3/R1 locus), and Chr.22q12 (HORMAD2 locus). These IgAN loci are associated with risk of other immune-mediated disorders such as type I diabetes, multiple sclerosis, or inflammatory bowel disease. We tested association of these loci in eight new independent cohorts of Asian, European, and African-American ancestry (N = 4,789), followed by meta-analysis with risk-score modeling in 12 cohorts (N = 10,755) and geospatial analysis in 85 world populations. Four susceptibility loci robustly replicated and all five loci were genome-wide significant in the combined cohort (P = 5×10⁻³²–3×10⁻¹⁰), with heterogeneity detected only at the PSMB9/TAP1 locus (I² = 0.60). Conditional analyses identified two new independent risk alleles within the HLA-DQB1/DRB1 locus, defining multiple risk and protective haplotypes within this interval. We also detected a significant genetic interaction, whereby the odds ratio for the HORMAD2 protective allele was reversed in homozygotes for a CFHR3/R1 deletion (P = 2.5×10⁻⁴). A seven–SNP genetic risk score, which explained 4.7% of overall IgAN risk, increased sharply with Eastward and Northward distance from Africa (r = 0.30, P = 3×10⁻¹²⁸). This model paralleled the known East–West gradient in disease risk. Moreover, the prediction of a South–North axis was confirmed by registry data showing that the prevalence of IgAN–attributable kidney failure is increased in Northern Europe, similar to multiple sclerosis and type I diabetes. Variation at IgAN susceptibility loci correlates with differences in disease prevalence among world populations. These findings inform genetic, biological, and epidemiological investigations of IgAN and permit cross-comparison with other complex traits that share genetic risk loci and geographic patterns with IgAN.     

Spatial variation of sequestered calcium in the multicellular stage of Dictyostelium discoideum as assayed by chlortetracycline fluorescence

We have used chlortetracycline (CTC) as a fluorescent probe to detect the distribution of sequestered calcium in multicellular stages of Dictyostelium discoideum. Tips of late aggregates, slugs and early culminating masses fluoresce very strongly. Most of the fluorescence is intracellular in origin and emanates from a small number of intense punctate sources. The sources correspond in part to autophagic vacuoles vis. neutral-red staining, acidic digestive vesicles, and may also include intracellular organelles; cytoplasmic fluorescence is much weaker in comparison. The level of fluorescence drops in the middle portion of slugs and rises again in the posteriormost region, though not to as high a level as in the tip. This holds good irrespective of whether CTC is applied only in the neighbourhood of the aggregate centre, only in the aggregate periphery, or to the whole aggregate. We infer that there must be a good deal of mixing in the stages leading from aggregation to slug formation; thus the serial order in which cells enter an aggregate does not bear any relation to their ultimate fates. The other implication of our study is that calcium sequestration is much more extensive in prestalk and anterior-like cells than in prespore cells. These findings are discussed with regard to possible implications for pattern formation.     

The use of historical environmental monitoring data to test predictions on cross-scale ecological responses to alterations in river flows

Determination of ecological responses to river flows is fundamental to understanding how flow-dependent ecosystems have been altered by regulation, water diversions and climate change, and how to effect river restoration. Knowledge of ecohydrological relationships can support water management and policy, but this is not always the case. Management rules have tended to be developed ahead of scientific knowledge. The lag between practice and knowledge could be addressed by using historical monitoring data on ecological responses to changes in flows to determine significant empirical ecohydrological relationships, as an adjunct to investigating responses prospectively. This possibility was explored in the Murray–Darling Basin, Australia. We assessed 359 data sets collected during monitoring programs across the basin. Of these, only 32 (9%) were considered useful, based on a match between the scale at which sampling was done and ecological responses are likely to occur, and used to test flow–ecology predictions for phytoplankton, macroinvertebrates, fishes, waterbirds, floodplain trees, basin-scale vegetation and estuarine biota. We found relationships between flow and ecological responses were likely to be more strongly supported for large, long-lived, widespread biota (waterbirds, basin-scale vegetation, native fishes), than for more narrowly distributed (e.g. estuarine fishes) or smaller, short-lived organisms (e.g. phytoplankton, macroinvertebrates). This pattern is attributed to a mismatch between the design of monitoring programs and the response time frames of individual biota and processes, and to the use of local river discharge as a primary predictor variable when, for many biotic groups, other predictors need to be considered.