Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species

Genic microsatellites or simple sequence repeat markers derived from expressed sequence tags (ESTs), referred to as EST–SSRs, are inexpensive to develop, represent transcribed genes, and often have assigned putative function. The large apple (Malus × domestica) EST database (over 300,000 sequences) provides a valuable resource for developing well-characterized DNA molecular markers. In this study, we have investigated the level of transferability of 68 apple EST–SSRs in 50 individual members of the Rosaceae family, representing three genera and 14 species. These representatives included pear (Pyrus communis), apricot (Prunus armeniaca), European plum (P. domestica), Japanese plum (P. salicina), almond (P. dulcis), peach (P. persica), sour cherry (P. cerasus), sweet cherry (P. avium), strawberry (Fragaria vesca, F. moschata, F. virginiana, F. nipponica, and F. pentaphylla), and rose (Rosa hybrida). All 68 primer pairs gave an amplification product when tested on eight apple cultivars, and for most, the genomic DNA-derived amplification product matched the expected size based on EST (in silico) data. When tested across members of the Rosaceae, 75% of these primer pairs produced amplification products. Transferability of apple EST–SSRs across the Rosaceae ranged from 25% in apricot to 59% in the closely related pear. Besides pear, the highest transferability of these apple EST–SSRs, at the genus level, was observed for strawberry and peach/almond, 49 and 38%, respectively. Three markers amplified in at least one genotype within all tested species, while eight additional markers amplified in all species, except for cherry. These 11 markers are deemed good candidates for a widely transferable Rosaceae marker set provided their level of polymorphism is adequate. Overall, these findings suggest that transferability of apple EST–SSRs across Rosaceae is varied, yet valuable, thereby providing additional markers for comparative mapping and for carrying out evolutionary studies.     

Elevated CO2 will not select for enhanced growth in white spruce despite genotypic variation in response

The effect of elevated atmospheric CO₂ on plant growth has been well-documented in the literature. However, few studies have quantified intra-specific genetic variation in growth response, and the potential for natural and artificial selection to act upon this variation. This study examined intra-specific variation in growth response to elevated CO₂ in 29 genotypes of white spruce (Picea glauca), a widely distributed and economically important species of the boreal forest region in North America. Trees were exposed to either ambient (370 μL L^?1) or twice-ambient CO₂ (740 μL L^?1). The opportunity for selection (i.e. the relative variation in fitness) was determined at low and high CO₂ levels with size as a measure of fitness and heritability of this variation determined. There was considerable variation among the genotypes in size and response to elevated CO₂. The increase in mass at elevated CO₂ ranged from 23% to 108% depending upon genotype. In spite of this variation, the genetic correlation between the two environments approached unity, as genotype variance was much greater than the genotype×CO₂ variance. Elevated CO₂ had no effect on heritability of the size-related traits we examined, and either had no effect on opportunity for selection, or decreased it. We conclude that selection at elevated atmospheric CO₂ is unlikely to increase mean plant size in white spruce beyond that observed for present day populations grown at elevated CO₂, despite the substantial genetic variation in CO₂ response displayed by this species.     

Differential grazing of two heterotrophic nanoflagellates on marine Synechococcus strains

Grazing of heterotrophic nanoflagellates on marine picophytoplankton presents a major mortality factor for this important group of primary producers. However, little is known of the selectivity of the grazing process, often merely being thought of as a general feature of cell size and motility. In this study, we tested grazing of two heterotrophic nanoflagellates, Paraphysomonas imperforata and Pteridomonas danica , on strains of marine Synechococcus . Both nanoflagellates proved to be selective in their grazing, with Paraphysomonas being able to grow on 5, and Pteridomonas on 11, of 37 Synechococcus strains tested. Additionally, a number of strains (11 for Paraphysomonas , 9 for Pteridomonas ) were shown to be ingested, but not digested (and thus did not support growth of the grazer). Both the range of prey strains that supported growth as well as those that were ingested but not digested was very similar for the two grazers, suggesting a common property of these prey strains that lent them susceptible to grazing. Subsequent experiments on selected Synechococcus strains showed a pronounced difference in grazing susceptibility between wild-type Synechococcus sp. WH7803 and a spontaneous phage-resistant mutant derivative, WH7803PHR, suggesting that cell surface properties of the Synechococcus prey are an important attribute influencing grazing vulnerability.     

On the stability of metabolic cycles

We investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of metabolic networks with certain structural regularities can be studied using a combination of analytical and computational techniques. We then apply these techniques to a class of single input, single output metabolic cycles, and find that the cycles are stable under all conditions tested. Next, we extend our analysis to a small autocatalytic cycle, and determine parameter regimes within which the cycle is very likely to be stable. We demonstrate that analytical methods can be used to understand the relationship between kinetic parameters and stability, and that results from these analytical methods can be confirmed with computational experiments. In addition, our results suggest that elevated metabolite concentrations and certain crucial saturation parameters can strongly affect the stability of the entire metabolic cycle. We discuss our results in light of the possibility that evolutionary forces may select for metabolic network topologies with a high intrinsic probability of being stable. Furthermore, our conclusions support the hypothesis that certain types of metabolic cycles may have played a role in the development of primitive metabolism despite the absence of regulatory mechanisms.     

Lactate formation in Caldicellulosiruptor saccharolyticus is regulated by the energy carriers pyrophosphate and ATP

Caldicellulosiruptor saccharolyticus displays superior H₂ yields on a wide range of carbon sources provided that lactate formation is avoided. Nevertheless, a low lactate flux is initiated as the growth rate declined in the transition to the stationary phase, which coincides with a drastic decrease in the glucose consumption and acetate production fluxes. In addition, the decrease in growth rate was accompanied by a sudden increase and then decrease in NADH levels. The V′_MAX of the lactate dehydrogenase (LDH) doubled when the cells entered the stationary phase. Kinetic analysis revealed that at the metabolic level LDH activity is regulated through (i) competitive inhibition by pyrophosphate (PPi, k_i=1.7 mM) and NAD (k_i=0.43 mM) and (ii) allosteric activation by FBP (300%), ATP (160%) and ADP (140%). From these data a MWC-based model was derived. Simulations with this model could explain the observed lactate shift by displaying how the sensitivity of LDH activity to NADH/NAD ratio varied with different PP_i concentrations. Moreover, the activation of LDH by ATP indicates that C. saccharolyticus uses LDH as a means to adjusts its flux of ATP and NADH production. To our knowledge, this is the first time PPi is observed as an effector of LDH.     

Genistein improves neuropathology and corrects behaviour in a mouse model of neurodegenerative metabolic disease

Background

Neurodegenerative metabolic disorders such as mucopolysaccharidosis IIIB (MPSIIIB or Sanfilippo disease) accumulate undegraded substrates in the brain and are often unresponsive to enzyme replacement treatments due to the impermeability of the blood brain barrier to enzyme. MPSIIIB is characterised by behavioural difficulties, cognitive and later motor decline, with death in the second decade of life. Most of these neurodegenerative lysosomal storage diseases lack effective treatments. We recently described significant reductions of accumulated heparan sulphate substrate in liver of a mouse model of MPSIIIB using the tyrosine kinase inhibitor genistein.

Methodology/Principal Findings

We report here that high doses of genistein aglycone, given continuously over a 9 month period to MPSIIIB mice, significantly reduce lysosomal storage, heparan sulphate substrate and neuroinflammation in the cerebral cortex and hippocampus, resulting in correction of the behavioural defects observed. Improvements in synaptic vesicle protein expression and secondary storage in the cerebral cortex were also observed.

Conclusions/Significance

Genistein may prove useful as a substrate reduction agent to delay clinical onset of MPSIIIB and, due to its multimodal action, may provide a treatment adjunct for several other neurodegenerative metabolic diseases.     

Fluid Phase Endocytic Uptake of Artificial Nano-Spheres and Fluorescent Quantum Dots by Sycamore Cultured Cells: Evidence for the Distribution of Solutes to Different Intracellular Compartments

Fluid phase endocytic uptake of external solutes in plant cells was further substantiated using artificial polystyrene nano-spheres (40 nm) and CdSe/ZnS quantum dots (20 nm). Both types of artificial nano-particles were taken up by sycamore-cultured cells. However, whereas polystyrene nano-spheres were delivered to the central vacuole, CdSe/ZnS nano-dots were sequestered into cytoplasmic vesicular structures. Using dextran-Texas Red (m.w. 3,000; d-TR) as additional marker, confocal micrographs confirmed the distinct topographic distribution of CdSe/ZnS quantum dots within the cell. Initially, d-TR and CdSe/ZnS quantum dots colocalized within cytoplasmic vesicles. After 18 h incubation, d-TR was distinctly localized in the vacuole whereas CdSe/ZnS quantum dots remained sequestered in cytoplasmic membranous compartments. The data provide a first evidence for the rapid distribution of solutes taken up by endocytosis to distinct intracellular compartments.Key Words: apoplast, assimilate partitioning, endocytosis, protoplasts, sucrose transport, sucrose uptake, vacuole     

Physician assistants and bioterrorism preparedness

Despite the resources dedicated since 2001 to training health providers in emergency and bioterrorism preparedness and response, the literature on the participation of physician assistants (PAs) is very limited. The purpose of this pilot study was to explore the training level and experiences of PAs in the diagnosis and treatment of chemical, biological, radiological, nuclear, and explosive agents that could be used in a bioterrorism attack. The study population consisted of licensed PAs in 37 northern Texas counties. Data were collected through mailed and web-based surveys. Response rate was 36%. More than half of the respondents (58.6%) had not participated in bioterrorism preparedness and response training. Results also indicated that the level of training has not increased since September 11, 2001. However, most respondents were receptive to the idea of participating in both preparedness training and response efforts. It is recommended that state agencies increase training opportunities for PAs in bioterrorism preparedness and response.     

Formation and nuclear export of preribosomes are functionally linked to the small-ubiquitin-related modifier pathway

Ribosomal precursor particles are initially assembled in the nucleolus prior to their transfer to the nucleoplasm and export to the cytoplasm. In a screen to identify thermosensitive (ts) mutants defective in the export of pre-60S ribosomal subunit, we isolated the rix16-1 mutant. In this strain, nucleolar accumulation of the Rpl25-eGFP reporter was complemented by UBA2 (a subunit of the E1 sumoylation enzyme). Mutations in UBC9 (E2 enzyme), ULP1 [small-ubiquitin-related modifier (SUMO) isopeptidase] and SMT3 (SUMO-1) caused 60S export defects. A directed analysis of the SUMO proteome revealed that many ribosome biogenesis factors are sumoylated. Importantly, preribosomal particles along both the 60S and the 40S synthesis pathways were decorated with SUMO, showing its direct involvement. Consistent with this, early 60S assembly factors were genetically linked to SUMO conjugation. Notably, the SUMO deconjugating enzyme Ulp1, which localizes to the nuclear pore complex (NPC), was functionally linked to the 60S export factor Mtr2. Together our data suggest that sumoylation of preribosomal particles in the nucleus and subsequent desumoylation at the NPC is necessary for efficient ribosome biogenesis and export in eukaryotes.     

Coordinated nuclear import of RNA polymerase III subunits

Eukaryotic RNA polymerases are multisubunit assemblies, whose enzymatic function in the nucleus is intensively studied. However, little is known about the biogenesis of the three RNA polymerases and coupling to nucleo-cytoplasmic transport. Here, we show that Rpc128, the second largest subunit of RNA polymerase III, was mislocalized to the cytoplasm, when a short sequence in the N-terminal domain was deleted. Importantly, nuclear import of other, but not all, RNA polymerase III subunits was impaired in this RPC128DeltaN mutant. These data suggest that RNA polymerase III subunits are not imported independently into the nucleus but may require preassembly into cytoplasmic subcomplexes for coordinated nuclear uptake. We expect these studies to be a starting point to dissect the complex biogenesis pathway of eukaryotic RNA polymerases.