X-linked cone-rod dystrophy (locus COD1): identification of mutations in RPGR exon ORF15

X-linked cone-rod dystrophy (COD1) is a retinal disease that primarily affects the cone photoreceptors; the disease was originally mapped to a limited region of Xp11.4. We evaluated the three families from our original study with new markers and clinically reassessed all key recombinants; we determined that the critical intervals in families 2 and 3 overlapped the RP3 locus and that a status change (from affected to probably unaffected) of a key recombinant individual in family 1 also reassigned the disease locus to include RP3 as well. Mutation analysis of the entire RPGR coding region identified two different 2-nucleotide (nt) deletions in ORF15, in family 2 (delAG) and in families 1 and 3 (delGG), both of which result in a frameshift leading to altered amino acid structure and early termination. In addition, an independent individual with X-linked cone-rod dystrophy demonstrated a 1-nt insertion (insA) in ORF15. The presence of three distinct mutations associated with the same disease phenotype provides strong evidence that mutations in RPGR exon ORF15 are responsible for COD1. Genetic heterogeneity was observed in three other families, including the identification of an in-frame 12-nt deletion polymorphism in ORF15 that did not segregate with the disease in one of these families.     

Widespread occurrence and genomic context of unusually small polyketide synthase genes in microbial consortia associated with marine sponges

Numerous marine sponges harbor enormous amounts of as-yet-uncultivated bacteria in their tissues. There is increasing evidence that these symbionts play an important role in the synthesis of protective metabolites, many of which are of great pharmacological interest. In this study, genes for the biosynthesis of polyketides, one of the most important classes of bioactive natural products, were systematically investigated in 20 demosponge species from different oceans. Unexpectedly, the sponge metagenomes were dominated by a ubiquitously present, evolutionarily distinct, and highly sponge-specific group of polyketide synthases (PKSs). Open reading frames resembling animal fatty acid genes were found on three corresponding DNA regions isolated from the metagenomes of Theonella swinhoei and Aplysina aerophoba. Their architecture suggests that methyl-branched fatty acids are the metabolic product. According to a phylogenetic analysis of housekeeping genes, at least one of the PKSs belongs to a bacterium of the Deinococcus-Thermus phylum. The results provide new insights into the chemistry of sponge symbionts and allow inference of a detailed phylogeny of the diverse functional PKS types present in sponge metagenomes. Based on these qualitative and quantitative data, we propose a significantly simplified strategy for the targeted isolation of biomedically relevant PKS genes from complex sponge-symbiont associations.     

Effects of agricultural production on phosphorus losses from paddy soils: a case study in the Taihu Lake Region of China

A field plot experiment was conducted on two types of paddy soils in the Taihu Lake Region of China from June 2000 through 2002 to assess phosphorus (P) losses by runoff and drainage flow and the effectiveness of rice–wheat double cropping on reducing P losses from paddy soils. Commercial NPK compound fertilizer and single superphosphate fertilizer were applied to furnish 0, 30, 150, and 300 kg P ha^–1 for rice season trials, and 0, 20, 80, and 160 kg P ha^–1 for wheat season trials. The experiments consisted of four replicates (plots of 5 × 6 m in a randomized block design) of each treatment in Argic stagnic anthrosols (Anzhen site) and six replicates in Cumulic stagnic anthrosols (Changshu site). P30 and P20 treatments (30 and 20 kg P ha^–1 in rice and wheat seasons, respectively) were considered as conventional P application rates in this area. Higher P treatments, such as P150 and P300 for rice and P80 and P160 for wheat, were intended to simulate the status of soil P in ~10–20 years with an application of P30 or P20 kg P ha^–1 each season. Results revealed that the average concentration of total P (TP) in runoff samples was 0.870 mg P l^–1 from P30 plots during the rice season, and 0.763 mg P l^–1 from P20 plots during the wheat season in both years at the Anzhen site, while it was 0.703 and 1.292 mg P l^–1, respectively, at the Changshu site. Average TP load (mass loss) at the Anzhen site with conventional P application rates was 220.9 and 439.5 g P ha^–1 during rice season in 2000/2001 and 2001/2002, respectively, but was 382.3 and 709.4g P ha^–1 during wheat season, respectively. Mass loss at the Changshu site was 140.4 and 165.7 g P ha^–1 during the rice season and 539.1 and 1184.6 g P ha^–1 during the wheat season, respectively. P losses from paddy soils were significantly greater during the wheat season, especially at the Changshu site, indicating that planting rice reduced P. Phosphate fertilizer levels significantly affected P concentrations and P loads in runoff both seasons. Both mean concentrations and average seasonal P loads from the P150/P80 plots were lower than that from the P300/P160 plots, but significantly higher than that from the P30/P20 and P0 plots. This implied that runoff P loads would be greatly increased in 10–20 years as a result of the accumulation of soil P if 50 kg P ha^–1 (rice season plus wheat season) is applied each year.     

The mouse gene encoding the carnitine biosynthetic enzyme 4-N-trimethylaminobutyraldehyde dehydrogenase is regulated by peroxisome proliferator-activated receptor α

Genes involved in carnitine uptake and synthesis, such as organic cation transporter-2 (OCTN2) and γ-butyrobetaine dioxygenase (BBD), have been shown to be regulated by peroxisome proliferator-activated receptor (PPAR)α directly. Whether other genes encoding enzymes involved in the carnitine synthesis pathway, such as 4-N-trimethylaminobutyraldehyde dehydrogenase (TMABA-DH) and trimethyllysine dioxygenase (TMLD), are also direct PPARα target genes is less clear. In silico-analysis of the mouse TMLD promoter and first intron and the TMABA-DH promoter revealed several putative peroxisome proliferator response elements (PPRE) with high similarity to the consensus PPRE. Luciferase reporter gene assays using either a 2kb TMLD promoter or a 4kb TMLD first intron reporter constructs revealed no functional PPRE. In contrast, reporter gene assays using wild-type and mutated 5′-truncation TMABA-DH promoter reporter constructs showed that one PPRE located at position -132 in the proximal promoter is probably functional. Using gel shift assays we observed in vitro-binding of PPARα to this PPRE. Moreover, using chromatin immunoprecipitation assays we found that PPARα also binds in vivo to a nucleotide sequence spanning the PPRE at -132, which confirms that this PPRE is functional. In conclusion, the present study shows that the mouse TMABA-DH gene is a direct PPARα target gene. Together with the recent identification of the mouse BBD and the mouse OCTN2 genes as PPARα target genes this finding confirm that PPARα plays a key role in the regulation of carnitine homeostasis by controlling genes involved in carnitine synthesis and carnitine uptake.     

Par-complex proteins promote proliferative progenitor divisions in the developing mouse cerebral cortex

The size of brain regions depends on the balance between proliferation and differentiation. During development of the mouse cerebral cortex, ventricular zone (VZ) progenitors, neuroepithelial and radial glial cells, enlarge the progenitor pool by proliferative divisions, while basal progenitors located in the subventricular zone (SVZ) mostly divide in a differentiative mode generating two neurons. These differences correlate to the existence of an apico-basal polarity in VZ, but not SVZ, progenitors. Only VZ progenitors possess an apical membrane domain at which proteins of the Par complex are strongly enriched. We describe a prominent decrease in the amount of Par-complex proteins at the apical surface during cortical development and examine the role of these proteins by gain- and loss-of-function experiments. Par3 (Pard3) loss-of-function led to premature cell cycle exit, reflected in reduced clone size in vitro and the restriction of the progeny to the lower cortical layers in vivo. By contrast, Par3 or Par6 (Pard6alpha) overexpression promoted the generation of Pax6+ self-renewing progenitors in vitro and in vivo and increased the clonal progeny of single progenitors in vitro. Time-lapse video microscopy revealed that a change in the mode of cell division, rather than an alteration of the cell cycle length, causes the Par-complex-mediated increase in progenitors. Taken together, our data demonstrate a key role for the apically located Par-complex proteins in promoting self-renewing progenitor cell divisions at the expense of neurogenic differentiation in the developing cerebral cortex.