Identical mutation in a novel retinal gene causes progressive rod-cone degeneration in dogs and retinitis pigmentosa in humans

Progressive rod-cone degeneration (prcd) is a late-onset, autosomal recessive photoreceptor degeneration of dogs and a homolog for some forms of human retinitis pigmentosa (RP). Previously, the disease-relevant interval was reduced to a 106-kb region on CFA9, and a common phenotype-specific haplotype was identified in all affected dogs from several different breeds and breed varieties. Screening of a canine retinal EST library identified partial cDNAs for novel candidate genes in the disease-relevant interval. The complete cDNA of one of these, PRCD, was cloned in dog, human, and mouse. The gene codes for a 54-amino-acid (aa) protein in dog and human and a 53-aa protein in the mouse; the first 24 aa, coded for by exon 1, are highly conserved in 14 vertebrate species. A homozygous mutation (TGC --> TAC) in the second codon shows complete concordance with the disorder in 18 different dog breeds/breed varieties tested. The same homozygous mutation was identified in a human patient from Bangladesh with autosomal recessive RP. Expression studies support the predominant expression of this gene in the retina, with equal expression in the retinal pigment epithelium, photoreceptor, and ganglion cell layers. This study provides strong evidence that a mutation in the novel gene PRCD is the cause of autosomal recessive retinal degeneration in both dogs and humans.     

Linkage disequilibrium mapping in domestic dog breeds narrows the progressive rod-cone degeneration interval and identifies ancestral disease-transmitting chromosome

Canine progressive rod-cone degeneration (prcd) is a retinal disease previously mapped to a broad, gene-rich centromeric region of canine chromosome 9. As allelic disorders are present in multiple breeds, we used linkage disequilibrium (LD) to narrow the approximately 6.4-Mb interval candidate region. Multiple dog breeds, each representing genetically isolated populations, were typed for SNPs and other polymorphisms identified from BACs. The candidate region was initially localized to a 1.5-Mb zero recombination interval between growth factor receptor-bound protein 2 (GRB2) and SEC14-like 1 (SEC14L). A fine-scale haplotype of the region was developed, which reduced the LD interval to 106 kb and identified a conserved haplotype of 98 polymorphisms present in all prcd-affected chromosomes from 14 different dog breeds. The findings strongly suggest that a common ancestor transmitted the prcd disease allele to many of the modern dog breeds and demonstrate the power of the LD approach in the canine model.     

Mutations disrupting selenocysteine formation cause progressive cerebello-cerebral atrophy

The essential micronutrient selenium is found in proteins as selenocysteine (Sec), the only genetically encoded amino acid whose biosynthesis occurs on its cognate tRNA in humans. In the final step of selenocysteine formation, the essential enzyme SepSecS catalyzes the conversion of Sep-tRNA to Sec-tRNA. We demonstrate that SepSecS mutations cause autosomal-recessive progressive cerebellocerebral atrophy (PCCA) in Jews of Iraqi and Moroccan ancestry. Both founder mutations, common in these two populations, disrupt the sole route to the biosynthesis of the 21st amino acid, Sec, and thus to the generation of selenoproteins in humans.     

Combined Effects of CO2 and Light on the N2-Fixing Cyanobacterium Trichodesmium IMS101: Physiological Responses

Recent studies on the diazotrophic cyanobacterium Trichodesmium erythraeum (IMS101) showed that increasing CO₂ partial pressure (pCO₂) enhances N₂ fixation and growth. Significant uncertainties remain as to the degree of the sensitivity to pCO₂, its modification by other environmental factors, and underlying processes causing these responses. To address these questions, we examined the responses of Trichodesmium IMS101 grown under a matrix of low and high levels of pCO₂ (150 and 900 μatm) and irradiance (50 and 200 μmol photons m⁻² s⁻¹). Growth rates as well as cellular carbon and nitrogen contents increased with increasing pCO₂ and light levels in the cultures. The pCO₂-dependent stimulation in organic carbon and nitrogen production was highest under low light. High pCO₂ stimulated rates of N₂ fixation and prolonged the duration, while high light affected maximum rates only. Gross photosynthesis increased with light but did not change with pCO₂. HCO₃⁻ was identified as the predominant carbon source taken up in all treatments. Inorganic carbon uptake increased with light, but only gross CO₂ uptake was enhanced under high pCO₂. A comparison between carbon fluxes in vivo and those derived from ¹³C fractionation indicates high internal carbon cycling, especially in the low-pCO₂ treatment under high light. Light-dependent oxygen uptake was only detected under low pCO₂ combined with high light or when low-light-acclimated cells were exposed to high light, indicating that the Mehler reaction functions also as a photoprotective mechanism in Trichodesmium. Our data confirm the pronounced pCO₂ effect on N₂ fixation and growth in Trichodesmium and further show a strong modulation of these effects by light intensity. We attribute these responses to changes in the allocation of photosynthetic energy between carbon acquisition and the assimilation of carbon and nitrogen under elevated pCO₂. These findings are supported by a complementary study looking at photosynthetic fluorescence parameters of photosystem II, photosynthetic unit stoichiometry (photosystem I:photosystem II), and pool sizes of key proteins in carbon and nitrogen acquisition.Human-induced climate change will significantly alter the marine environment within the next century and beyond. Future scenarios predict an increase from currently approximately 380 to about 750 to 1,000 μatm CO₂ partial pressure (pCO₂) in the atmosphere until the end of this century (Raven et al., 2005; Raupach et al., 2007). As the ocean takes up this anthropogenic CO₂, dissolved inorganic carbon (DIC) in the surface ocean increases while the pH decreases (Wolf-Gladrow et al., 1999). Rising global temperatures will increase surface ocean stratification, which may affect the light regime in the upper mixed layer as well as nutrient input from deeper waters (Doney, 2006). Uncertainties remain regarding both the magnitude of the physicochemical changes and the biological responses of organisms, including species and populations of the oceanic primary producers at the basis of the food webs.In view of potential ecological implications and feedbacks on climate, several studies have examined pCO₂ sensitivity in phytoplankton key species (Burkhardt and Riebesell, 1997; Riebesell et al., 2000; Rost et al., 2003; Tortell et al., 2008). Pronounced responses to elevated pCO₂ were observed in N₂-fixing cyanobacteria (Barcelos é Ramos et al., 2007; Hutchins et al., 2007; Levitan et al., 2007; Fu et al., 2008; Kranz et al., 2009), which play a vital role in marine ecosystems by providing a new source of biologically available nitrogen species to otherwise nitrogen-limited regions. Recent studies focused on the impact of different environmental factors on the filamentous Trichodesmium species, which is known for high abundance and the formation of massive blooms in tropical and subtropical areas (Capone et al., 2005; Mahaffey et al., 2005). Higher pCO₂ levels stimulated growth rates, biomass production, and N₂ fixation (Hutchins et al., 2007; Levitan et al., 2007; Kranz et al., 2009) and affected inorganic carbon acquisition of the cells (Kranz et al., 2009). While elevated sea surface temperatures are predicted to shift the spatial distribution of Trichodesmium species toward higher latitudes (Breitbarth et al., 2007), the combined effects of pCO₂ and temperature may favor this species and extend its niche even farther (Hutchins et al., 2007; Levitan et al., 2010a). An increase in the average light intensity, caused by the predicted shoaling of the upper mixed layer, may further stimulate photosynthesis and thus growth and N₂ fixation of Trichodesmium (Breitbarth et al., 2008). To our knowledge, the combined effects of light and pCO₂ have not been studied yet, although these environmental factors are likely to influence photosynthesis and other key processes in Trichodesmium.To understand the responses of an organism to changes in environmental conditions, metabolic processes must be studied. In Trichodesmium, photosynthetically generated energy (ATP and NADPH) is primarily used for the fixation of CO₂ in the Calvin-Benson cycle. A large proportion of this energy, however, is also required for the process of N₂ fixation via nitrogenase and for the operation of a CO₂-concentrating mechanism (CCM). The latter involves active uptake of inorganic carbon, which functions to increase the rate of carboxylation reaction mediated by Rubisco. This ancient and highly conserved enzyme is characterized by low affinities for its substrate CO₂ and a susceptibility to a competing reaction with oxygen (O₂) as substrate (Badger et al., 1998); the latter initiates photorespiration. As cyanobacterial Rubisco possesses one of the lowest CO₂ affinities among phytoplankton (Badger et al., 1998), a considerable amount of resources have to be invested to achieve sufficient rates of carbon fixation and to avoid photorespiration. A first step toward a mechanistic understanding of responses in Trichodesmium has been taken by Levitan et al. (2007), focusing on pCO₂ dependency of nitrogenase activity and photosynthesis. Subsequently, Kranz et al. (2009) described variations in CCM efficiency with pCO₂ and suggested that the observed plasticity in CCM regulation allowed energy reallocation under high pCO₂, which may explain the observed pCO₂-dependent changes in nitrogenase activity, growth, and elemental composition (Barcelos é Ramos et al., 2007; Hutchins et al., 2007; Levitan et al., 2007).In this study, we measured growth responses as well as metabolic key processes in Trichodesmium erythraeum (IMS101) under environmental conditions that likely alter the energy budget and/or energy allocation of the cell. Cultures were acclimated to a matrix of low and high pCO₂ (150 and 900 μatm) at two different light intensities (50 and 200 μmol photons m⁻² s⁻¹). For each of the four treatments, changes in growth rates, elemental ratios, and the accumulation of particulate carbon and nitrogen were measured. Metabolic processes (gross photosynthesis, CCM activity, and O₂ uptake) were obtained by means of membrane-inlet mass spectrometry (MIMS), while N₂ fixation was detected by gas chromatography. As these processes may vary over the diurnal cycle in Trichodesmium (Berman-Frank et al., 2001; Kranz et al., 2009), measurements were performed in the morning and around midday. The results on metabolic processes were accompanied by measurements of the fluorescence of PSII, ratios of the photosynthetic units (PSI:PSII), and pool sizes of key proteins involved in carbon and nitrogen fixation as well as assimilation (Levitan et al., 2010b).     

A dissipative particle dynamics model of carbon nanotubes

A mesoscale dissipative particle dynamics model of single wall carbon nanotubes (CNTs) is designed and demonstrated. The coarse-grained model is produced by grouping together carbon atoms and by bonding the new lumped particles through pair and triplet forces. The mechanical properties of the simulated tube are determined by the bonding forces, which are derived by virtual experiments. Through the introduction of van der Waals interactions, tube–tube interactions were studied. Owing to the reduced number of particles, this model allows the simulation of relatively large systems. The applicability of the presented scheme to model CNT based mechanical devices is discussed.     

A conserved F box regulatory complex controls proteasome activity in Drosophila

The ubiquitin-proteasome system catalyzes the degradation of intracellular proteins. Although ubiquitination of proteins determines their stabilities, there is growing evidence that proteasome function is also regulated. We report the functional characterization of a conserved proteasomal regulatory complex. We identified DmPI31 as a binding partner of the F box protein Nutcracker, a component of an SCF ubiquitin ligase (E3) required for caspase activation during sperm differentiation in Drosophila. DmPI31 binds Nutcracker via a conserved mechanism that is also used by mammalian FBXO7 and PI31. Nutcracker promotes DmPI31 stability, which is necessary for caspase activation, proteasome function, and sperm differentiation. DmPI31 can activate 26S proteasomes in vitro, and increasing DmPI31 levels suppresses defects caused by diminished proteasome activity in vivo. Furthermore, loss of DmPI31 function causes lethality, cell-cycle abnormalities, and defects in protein degradation, demonstrating that DmPI31 is physiologically required for normal proteasome activity.     

Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression

This report provides a global view of how gene expression is affected by DNA replication. We analyzed synchronized cultures of Saccharomyces cerevisiae under conditions that prevent DNA replication initiation without delaying cell cycle progression. We use a higher‐order singular value decomposition to integrate the global mRNA expression measured in the multiple time courses, detect and remove experimental artifacts and identify significant combinations of patterns of expression variation across the genes, time points and conditions. We find that, first, ～88% of the global mRNA expression is independent of DNA replication. Second, the requirement of DNA replication for efficient histone gene expression is independent of conditions that elicit DNA damage checkpoint responses. Third, origin licensing decreases the expression of genes with origins near their 3′ ends, revealing that downstream origins can regulate the expression of upstream genes. This confirms previous predictions from mathematical modeling of a global causal coordination between DNA replication origin activity and mRNA expression, and shows that mathematical modeling of DNA microarray data can be used to correctly predict previously unknown biological modes of regulation.