Catalytic activities, molecular connections, and biological functions of plant RNA exosome complexes

RNA exosome complexes provide the main 3'-5'-exoribonuclease activities in eukaryotic cells and contribute to the maturation and degradation of virtually all types of RNA. RNA exosomes consist of a conserved core complex that associates with exoribonucleases and with multimeric cofactors that recruit the enzyme to its RNA targets. Despite an overall high level of structural and functional conservation, the enzymatic activities and compositions of exosome complexes and their cofactor modules differ among eukaryotes. This review highlights unique features of plant exosome complexes, such as the phosphorolytic activity of the core complex, and discusses the exosome cofactors that operate in plants and are dedicated to the maturation of ribosomal RNA, the elimination of spurious, misprocessed, and superfluous transcripts, or the removal of mRNAs cleaved by the RNA-induced silencing complex and other mRNAs prone to undergo silencing.

Polarized phonons carry angular momentum in ultrafast demagnetization

Magnetic phenomena are ubiquitous in nature and indispensable for modern science and technology, but it is notoriously difficult to change the magnetic order of a material in a rapid way. However, if a thin nickel film is subjected to ultrashort laser pulses, it loses its magnetic order almost completely within femtosecond timescales¹. This phenomenon is widespread^2-7 and offers opportunities for rapid information processing^8-11 or ultrafast spintronics at frequencies approaching those of light^8,9,12. Consequently, the physics of ultrafast demagnetization is central to modern materials research^1-7,13-28, but a crucial question has remained elusive: if a material loses its magnetization within mere femtoseconds, where is the missing angular momentum in such a short time? Here we use ultrafast electron diffraction to reveal in nickel an almost instantaneous, long-lasting, non-equilibrium population of anisotropic high-frequency phonons that appear within 150-750 fs. The anisotropy plane is perpendicular to the direction of the initial magnetization and the atomic oscillation amplitude is 2 pm. We explain these observations by means of circularly polarized phonons that quickly absorb the angular momentum of the spin system before macroscopic sample rotation. The time that is needed for demagnetization is related to the time it takes to accelerate the atoms. These results provide an atomistic picture of the Einstein-de Haas effect and signify the general importance of polarized phonons for non-equilibrium dynamics and phase transitions.

SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis

SERRATE/ARS2 is a conserved RNA effector protein involved in transcription, processing and export of different types of RNAs. In Arabidopsis, the best-studied function of SERRATE (SE) is to promote miRNA processing. Here, we report that SE interacts with the nuclear exosome targeting (NEXT) complex, comprising the RNA helicase HEN2, the RNA binding protein RBM7 and one of the two zinc-knuckle proteins ZCCHC8A/ZCCHC8B. The identification of common targets of SE and HEN2 by RNA-seq supports the idea that SE cooperates with NEXT for RNA surveillance by the nuclear exosome. Among the RNA targets accumulating in absence of SE or NEXT are miRNA precursors. Loss of NEXT components results in the accumulation of pri-miRNAs without affecting levels of miRNAs, indicating that NEXT is, unlike SE, not required for miRNA processing. As compared to se-2, se-2 hen2-2 double mutants showed increased accumulation of pri-miRNAs, but partially restored levels of mature miRNAs and attenuated developmental defects. We propose that the slow degradation of pri-miRNAs caused by loss of HEN2 compensates for the poor miRNA processing efficiency in se-2 mutants, and that SE regulates miRNA biogenesis through its double contribution in promoting miRNA processing but also pri-miRNA degradation through the recruitment of the NEXT complex.

RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis

The RNA exosome is a key 3’−5’ exoribonuclease with an evolutionarily conserved structure and function. Its cytosolic functions require the co-factors SKI7 and the Ski complex. Here we demonstrate by co-purification experiments that the ARM-repeat protein RESURRECTION1 (RST1) and RST1 INTERACTING PROTEIN (RIPR) connect the cytosolic Arabidopsis RNA exosome to the Ski complex. rst1 and ripr mutants accumulate RNA quality control siRNAs (rqc-siRNAs) produced by the post-transcriptional gene silencing (PTGS) machinery when mRNA degradation is compromised. The small RNA populations observed in rst1 and ripr mutants are also detected in mutants lacking the RRP45B/CER7 core exosome subunit. Thus, molecular and genetic evidence supports a physical and functional link between RST1, RIPR and the RNA exosome. Our data reveal the existence of additional cytosolic exosome co-factors besides the known Ski subunits. RST1 is not restricted to plants, as homologues with a similar domain architecture but unknown function exist in animals, including humans.

Cytosolic RNA degradation by the RNA exosome requires the Ski complex. Here the authors show that the proteins RST1 and RIPR assist the RNA exosome and the Ski complex in RNA degradation, thereby preventing the production of secondary siRNAs from endogenous mRNAs.

Kinetics of Pulmonary Leukocyte Sequestration in Man during Hemodialysis with Different Membrane-Types

Although it has been suggested that pulmonary sequestration of leukocytes could account for membrane-dependent white blood cell depletion in HD, direct evidence in patients is still lacking. Therefore a study was initiated to test whether and how leukocytes distribute in the lung circulation during HD with different membranes. Thirteen patients suffering from chronic renal failure underwent lung scintigraphy during HD with cuprophane (n = 3), hemophane (n = 8) and polysulfone (n = 2) lowflux capillary dialyzers. Isolated autologous leukocytes were labelled with 99m-Technetium and reinfused before starting HD. Distribution of leukocyte related activity was registered by lung scintigraphy. In comparison to normal lung scintigraphy performed without HD, an impressive redistribution peak was demonstrated 10-20 min after the start of HD with cuprophane and also to a lesser extent with hemophane. When HD was performed with polysulfone the decrease in activity was delayed but no real redistribution was obtained.

In accordance with other phenomena, such as peripheral leukopenia and changes in granulocyte oxidative metabolism, pulmonary sequestration of leukocytes takes place in man in the initial phase of HD and appears to be strongly dependent on the type of membrane. (Int J Artif Organs 1990; 13: 729-36)

On-line Monitoring of the Intravascular Volume during Haemodialysis by Continuous Refractometry

The control of intravascular volume (IVV) by continuous on-line measurement of protein concentration would optimise the patients’ specific rate of ultrafiltration.

To prove the accuracy of a refractometric device, plasma was continuously drawn by haemofiltration during 10 haemodialysis treatments of male patients. Refractometry reflects highly significant changes in the concentrations of filtrate proteins (r = 0.862, p < 0.001) and blood proteins (rtotal = 0.593, ptotal < 0.001). In vitro, the refractometric device detected a change of protein concentration of 0.041 g/L through a refraction increase of 0.1 mV. The power of discrimination was 0.067 % of IVV. However, in vivo, the accuracy of IVV refractometric monitoring is reduced by interference factors such as sodium (0.141 mV/mmol/L), glucose (0.034 mV/mg/dl) and triglycerides (–0.040 mV/mg/dl). Adjustment of the refraction data using sodium and glucose electrodes and plasma filters with a cutoff below the size of chylomicrons is recommended.

Continuous Ionography (CIG) in Haemodialysis by Ion-Selective Carrier Membrane Electrodes (ISCME) with Solid Cement Contact for Flow-Through Measurement

Ion balance is of particular interest for patients maintained on RDT because of the importance of controlling ion movement and ion removal during haemodialysis. Continuous ionography (CIG) was therefore tested for electrolyte monitoring in extracorporeal haemodialysis in vitro and in vivo. The accuracy and stability of the electrodes were examined and various concentrations of potassium in blood, ultrafiltrate and dialysate were evaluated. Ion selective carrier membrane electrodes (ISCME) appeared to be suitable for continuous and simultaneous measurement of ions in blood and dialysis fluid. CIG monitoring of ion movement and ion removal could be the basis for adjusting and computer-managing ion elimination during extracorporeal haemodialysis.

RNA degradation by the plant RNA exosome involves both phosphorolytic and hydrolytic activities

The RNA exosome provides eukaryotic cells with an essential 3'-5' exoribonucleolytic activity, which processes or eliminates many classes of RNAs. Its nine-subunit core (Exo9) is structurally related to prokaryotic phosphorolytic exoribonucleases. Yet, yeast and animal Exo9s have lost the primordial phosphorolytic capacity and rely instead on associated hydrolytic ribonucleases for catalytic activity. Here, we demonstrate that Arabidopsis Exo9 has retained a distributive phosphorolytic activity, which contributes to rRNA maturation processes, the hallmark of exosome function. High-density mapping of 3' extremities of rRNA maturation intermediates reveals the intricate interplay between three exoribonucleolytic activities coordinated by the plant exosome. Interestingly, the analysis of RRP41 protein diversity across eukaryotes suggests that Exo9's intrinsic activity operates throughout the green lineage, and possibly in some earlier-branching non-plant eukaryotes. Our results reveal a remarkable evolutionary variation of this essential RNA degradation machine in eukaryotes.

Effective PEGylation of gold nanorods

Standard procedures to coat gold nanorods (AuNR) with poly(ethylene glycol) (PEG)-based ligands are not reliable and high PEG-grafting densities are not achieved. In this work, the ligand exchange of AuNR with PEGMUA, a tailored PEG-ligand bearing a C10 alkylene spacer, is studied. PEGMUA provides AuNR with very high stability against oxidative etching with cyanide. This etching reaction is utilized to study the ligand exchange in detail. Ligand exchange is faster, less ligand consuming and more reproducible with assisting chloroform extraction. Compared to PEG ligands commonly used, PEGMUA provides much higher colloidal and chemical stability. Further analyses based on NMR-, IR- and UV/Vis-spectroscopy reveal that significantly higher PEG-grafting densities, up to ∼3 nm(-2), are obtained with PEGMUA. This demonstrates how the molecular structure of the PEG ligand can be used to dramatically improve the ligand exchange and to synthesize PEGylated AuNR with high chemical and colloidal stability and high PEG grafting densities. Such AuNR are especially interesting for applications in nanomedicine.

The Zinc-Finger Protein SOP1 Is Required for a Subset of the Nuclear Exosome Functions in Arabidopsis

Correct gene expression requires tight RNA quality control both at transcriptional and post-transcriptional levels. Using a splicing-defective allele of PASTICCINO2 (PAS2), a gene essential for plant development, we isolated suppressor mutations modifying pas2-1 mRNA profiles and restoring wild-type growth. Three suppressor of pas2 (sop) mutations modified the degradation of mis-spliced pas2-1 mRNA species, allowing the synthesis of a functional protein. Cloning of the suppressor mutations identified the core subunit of the exosome SOP2/RRP4, the exosome nucleoplasmic cofactor SOP3/HEN2 and a novel zinc-finger protein SOP1 that colocalizes with HEN2 in nucleoplasmic foci. The three SOP proteins counteract post-transcriptional (trans)gene silencing (PTGS), which suggests that they all act in RNA quality control. In addition, sop1 mutants accumulate some, but not all of the misprocessed mRNAs and other types of RNAs that are observed in exosome mutants. Taken together, our data show that SOP1 is a new component of nuclear RNA surveillance that is required for the degradation of a specific subset of nuclear exosome targets.

SKI2 mediates degradation of RISC 5'-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis

Small regulatory RNAs are fundamental in eukaryotic and prokaryotic gene regulation. In plants, an important element of post-transcriptional control is effected by 20–24 nt microRNAs (miRNAs) and short interfering RNAs (siRNAs) bound to the ARGONAUTE1 (AGO1) protein in an RNA induced silencing complex (RISC). AGO1 may cleave target mRNAs with small RNA complementarity, but the fate of the resulting cleavage fragments remains incompletely understood. Here, we show that SKI2, SKI3 and SKI8, subunits of a cytoplasmic cofactor of the RNA exosome, are required for degradation of RISC 5′, but not 3′-cleavage fragments in Arabidopsis. In the absence of SKI2 activity, many miRNA targets produce siRNAs via the RNA-dependent RNA polymerase 6 (RDR6) pathway. These siRNAs are low-abundant, and map close to the cleavage site. In most cases, siRNAs were produced 5′ to the cleavage site, but several examples of 3′-spreading were also identified. These observations suggest that siRNAs do not simply derive from RDR6 action on stable 5′-cleavage fragments and hence that SKI2 has a direct role in limiting secondary siRNA production in addition to its function in mediating degradation of 5′-cleavage fragments.

A 1-Year Quantitative Survey of Noro-, Adeno-, Human Boca-, and Hepatitis E Viruses in Raw and Secondarily Treated Sewage from Two Plants in Norway

A study of enteric viruses in raw and treated sewage from two secondary treatment plants, which received sewage from Oslo city (plant A) and small municipalities in Hedmark county in Norway (plant B), showed high levels of noro-, adeno-, and bocavirus throughout the year. A seasonal variation was observed for adeno- and GII norovirus with higher levels during winter and bocavirus that had more positive samples during winter. The virus concentrations in raw sewage were comparable in the two plants, with medians (log10 genome copies per liter) of 6.1, 6.3, 6.0, and 4.5 for noro GI, noro GII, adeno-, and bocavirus, respectively. The level of hepatitis E virus was not determined as it was below the limit of quantification. The mean log10 virus reduction was 0.55 (plant A) and 1.44 (plant B) with the highest reduction found in the plant with longer hydraulic retention time. The adenoviruses were dominantly serotype 41, while serotype 12 appeared sporadically. Of the 102 raw and treated sewage samples that were tested, eight were positive for hepatitis E virus of which four were from treated sewage. Two of the four obtained gene sequences from hepatitis E virus originated from the rural sewage samples and showed high similarity with a genotype 3 strain of hepatitis E virus detected in local piglets. Two other hepatitis E virus sequences obtained from urban sewage samples showed high similarities with genotype 3 strains isolated from urban sewage in Spain and a human genotype 1 isolate from India. The study gives information on the levels of noroviruses in raw and treated sewage, which is valuable to risk assessment, information indicating that some infections with hepatitis E viruses in Norway have a regional origin and that human bocavirus 2 and 3 are prevalent in the Norwegian population.

Clinical value of the renal protein clearance determination

The clinical applicability of the determiniation of selectivity in proteinuria in the traditional way is limited. The methodological apparatus has to be relatively completed to get predicative results. Simplified procedures, e.g. determination according to two proteins only, have not proven to be useful in our hands. Screening tests such as disc electrophoresis have to precede the determinations. In special clinical problems, e.g. the question of steroid sensitiveness in morphological forms of glomerulonephritis, which supposedly do not respond to steroids according to the results of prospective studies, or as a parameter in observing the follow up of a disease, protein clearances may be a valuable diagnostic help.

The RNA helicases AtMTR4 and HEN2 target specific subsets of nuclear transcripts for degradation by the nuclear exosome in Arabidopsis thaliana

The RNA exosome is the major 3'-5' RNA degradation machine of eukaryotic cells and participates in processing, surveillance and turnover of both nuclear and cytoplasmic RNA. In both yeast and human, all nuclear functions of the exosome require the RNA helicase MTR4. We show that the Arabidopsis core exosome can associate with two related RNA helicases, AtMTR4 and HEN2. Reciprocal co-immunoprecipitation shows that each of the RNA helicases co-purifies with the exosome core complex and with distinct sets of specific proteins. While AtMTR4 is a predominantly nucleolar protein, HEN2 is located in the nucleoplasm and appears to be excluded from nucleoli. We have previously shown that the major role of AtMTR4 is the degradation of rRNA precursors and rRNA maturation by-products. Here, we demonstrate that HEN2 is involved in the degradation of a large number of polyadenylated nuclear exosome substrates such as snoRNA and miRNA precursors, incompletely spliced mRNAs, and spurious transcripts produced from pseudogenes and intergenic regions. Only a weak accumulation of these exosome substrate targets is observed in mtr4 mutants, suggesting that MTR4 can contribute, but plays rather a minor role for the degradation of non-ribosomal RNAs and cryptic transcripts in Arabidopsis. Consistently, transgene post-transcriptional gene silencing (PTGS) is marginally affected in mtr4 mutants, but increased in hen2 mutants, suggesting that it is mostly the nucleoplasmic exosome that degrades aberrant transgene RNAs to limit their entry in the PTGS pathway. Interestingly, HEN2 is conserved throughout green algae, mosses and land plants but absent from metazoans and other eukaryotic lineages. Our data indicate that, in contrast to human and yeast, plants have two functionally specialized RNA helicases that assist the exosome in the degradation of specific nucleolar and nucleoplasmic RNA populations, respectively.

Zur Wirkung von N-Methyl-N-β-chloräthylhydrazin und seinem Benzaldehydhydrazon auf die RNA -und Proteinsynthese sowie Stoffwechsel von synchronisierten Hefezellen / Effect of N-Methyl-N-β-chloroethylhydrazine and Its Benzaldehydhydrazone on RNA- and Protein Synthesis as Soon as Metabolism of Synchronously Growing Yeast Cells ( Saccharomyces cerevisiae)

N-methyl-N-β-chloroethylhydrazine and its benzaldehydhydrazone inhibit the influx of [6-3H]- uracil and ʟ- [U-14C] leucin in yeast cells as well as the incorporation in RNA and protein. Experi­ments with synchronously and asynchronously growing cells showed the N-methyl-N-β-chloroethyl- hydrazine essentially influences the dividing phase while the benzaldehydhydrazone is more ef­fective in the growthphase. The effect of these two substances on respiration, glycolysis and the concentration of fructose-1,6-diphosphate, triose phosphate, and adenosine triphosphate is small.

Über den biologischen Einfluß von N-Methyl-N-β-chloräthylhydrazin und seinem Benzaldehydhydrazon auf Hefezellen ( Saccharomyces cerevisiae) / Effect of N-Methyl-N-β-chloroethyl-hydrazine-HCl on the Growth and Multiplication of Yeast Cells (Saccharomyces cerevisiae)

N-Methyl-N-β-chloroethyl-hydrazine-HCl and its benzaldehydhydrazone inhibit growth and multi­plication of yeast cells. The DNA-synthesis is partially blocked. After removal of the substances the rate of this synthesis is much more increased than that of RNA and protein. The both sub­ stances we tested are more effective than simple alkylhydrazines.

Regulation glykolytischen Umsatzes durch Synthese und Abbau von Enzymen Regulation of Glycolysis by the Synthesis and Degradation of Enzymes

Differential derepression of the genome of potato tuber cells causes the onset of a vigorous metabolic activity, which is initiated by rapid synthesis of different RNA species, various proteins and phospholipids. Consequently enhanced respiration and the build up of cell compartments such as ribosomes and mitochondria as well as the performance of cell divisions and suberization of new-formed cell walls occur. Although there is an activation of metabolism in general with a concomitant rise in concentration of most glycolytic metabolites — as was proved for fructose-1.6-diphosphate, dihydroxyacetone, glyceraldehade-3-phosphate, phosphoenolepyruvate and pyruvate — the activities of the corresponding enzymes do not reflect these uniform metabolic changes. Aldolase and in a pronounced manner enolase and glutamate — pyruvate — transaminase lower their activities suddenly after derepression. The activity of triosephosphateisomerase remains constant. In contrast phosphoglyceromutase, pyruvate kinase and to a lower extent malic enzyme enhance their action during the same time.

Without doubt, differential lowering and enhancing the activity of glycolytic chain constituents at the same time is an important regulatory mechanism of the cell. The activation represents de novo synthesis of the protein concerned whereas the inactivation depends largely on protein synthesis. This is clearly shown by experiments with inhibitors of protein synthesis.

It is proposed that this differential synthesis and degradation represent a “long-time-regulation” of enzymatic activity of the cell in contrast to the known “short-time-regulation” by feedback or competition.

Ongoing hepatitis A outbreak in Europe 2013 to 2014: imported berry mix cake suspected to be the source of infection in Norway

On 7 March 2014, an increase in hepatitis A virus (HAV) infections was identified in Norway. As of 12 April, 19 cases of HAV infection with a virus strain identical to an ongoing European outbreak have been identified. Six probable cases are currently under investigation. On 11 April, a frozen berry mix cake imported from another European country was found as the likely source of the outbreak; the importer has withdrawn the product in Norway.

Uridylation prevents 3' trimming of oligoadenylated mRNAs

Degradation of mRNAs is usually initiated by deadenylation, the shortening of long poly(A) tails to oligo(A) tails of 12–15 As. Deadenylation leads to decapping and to subsequent 5′ to 3′ degradation by XRN proteins, or alternatively 3′ to 5′ degradation by the exosome. Decapping can also be induced by uridylation as shown for the non-polyadenylated histone mRNAs in humans and for several mRNAs in Schizosaccharomyces pombe and Aspergillus nidulans. Here we report a novel role for uridylation in preventing 3′ trimming of oligoadenylated mRNAs in Arabidopsis. We show that oligo(A)-tailed mRNAs are uridylated by the cytosolic UTP:RNA uridylyltransferase URT1 and that URT1 has no major impact on mRNA degradation rates. However, in absence of uridylation, oligo(A) tails are trimmed, indicating that uridylation protects oligoadenylated mRNAs from 3′ ribonucleolytic attacks. This conclusion is further supported by an increase in 3′ truncated transcripts detected in urt1 mutants. We propose that preventing 3′ trimming of oligo(A)-tailed mRNAs by uridylation participates in establishing the 5′ to 3′ directionality of mRNA degradation. Importantly, uridylation prevents 3′ shortening of mRNAs associated with polysomes, suggesting that a key biological function of uridylation is to confer 5′ to 3′ polarity in case of co-translational mRNA decay.

P5-11-17: Evaluating Tumor Heterogeneity in Immunohistochemistry Stained Breast Cancer Tissue

Context: Quantitative clinical measurement of heterogeneity in immunohistochemistry staining would be useful in both evaluating patient therapeutic response and identifying underlying issues in histopathology laboratory quality control.

Objective: To create a heterogeneity scoring approach (HetMap) that allows the visualization of an individual patient's IHC heterogeneity in the context of a population.

Design: We combined HER2 semi-quantitative analysis with the use of ecology diversity statistics to evaluate cell-level heterogeneity (consistency of protein expression within neighboring cells in a tumor nest) and tumor-level heterogeneity (differences of protein expression across a tumor as represented by a tissue section). We evaluated the approach on HER2 immunohistochemistry stained breast cancer samples, using 200 specimens across two different CLIA laboratories, with three pathologists at each laboratory each outlining regions of tumor for scoring by automatic cell-based image analysis. HetMap was evaluated using three different scoring schemes: HER2 scoring according to ASCO/CAP guidelines, H-Score and a new continuous HER2 score (HER2cont).

Results: Two definitions of heterogeneity, cell-level and tumor-level, provided useful independent measures of heterogeneity. Cell-level heterogeneity, reported either as an average or the maximum area of heterogeneity across a slide, had low levels of dependency on the pathologist choice of region (coefficient of variation of 15%). Tumor-level heterogeneity measurements had more dependence on the pathologist choice of regions (coefficient of variation of 25%). Results were highly similar between the two laboratories, which is encouraging for HER2 standardization, as the labs involved different pathologists, different specimens, and different standardization procedures, although both complied with CLIA/CAP guidelines for HER2 testing.

Conclusions: HetMap is a measure of heterogeneity, by which pathologists, oncologists, and drug development organizations can view cell-level and tumor-level heterogeneity for a patient for a given marker in the context of an entire patient cohort. Heterogeneity analysis can be a useful means to identify tumors with higher degrees of heterogeneity, or to highlight slides that should be rechecked for QC issues.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-11-17.

MTR4, a putative RNA helicase and exosome co-factor, is required for proper rRNA biogenesis and development in Arabidopsis thaliana

The exosome is a conserved protein complex that is responsible for essential 3'→5' RNA degradation in both the nucleus and the cytosol. It is composed of a nine-subunit core complex to which co-factors confer both RNA substrate recognition and ribonucleolytic activities. Very few exosome co-factors have been identified in plants. Here, we have characterized a putative RNA helicase, AtMTR4, that is involved in the degradation of several nucleolar exosome substrates in Arabidopsis thaliana. We show that AtMTR4, rather than its closely related protein HEN2, is required for proper rRNA biogenesis in Arabidopsis. AtMTR4 is mostly localized in the nucleolus, a subcellular compartmentalization that is shared with another exosome co-factor, RRP6L2. AtMTR4 and RRP6L2 cooperate in several steps of rRNA maturation and surveillance, such as processing the 5.8S rRNA and removal of rRNA maturation by-products. Interestingly, degradation of the Arabidopsis 5' external transcribed spacer (5' ETS) requires cooperation of both the 5'→3' and 3'→5' exoribonucleolytic pathways. Accumulating AtMTR4 targets give rise to illegitimate small RNAs; however, these do not affect rRNA metabolism or contribute to the phenotype of mtr4 mutants. Plants lacking AtMTR4 are viable but show several developmental defects, including aberrant vein patterning and pointed first leaves. The mtr4 phenotype resembles that of several ribosomal protein and nucleolin mutants, and may be explained by delayed ribosome biogenesis, as we observed a reduced rate of rRNA accumulation in mtr4 mutants. Taken together, these data link AtMTR4 with rRNA biogenesis and development in Arabidopsis.

Effects of aerobic exercise training on cognitive function and cortical vascularity in monkeys

This study examined whether regular exercise training, at a level that would be recommended for middle-aged people interested in improving fitness could lead to improved cognitive performance and increased blood flow to the brain in another primate species. Adult female cynomolgus monkeys were trained to run on treadmills for 1 h a day, 5 days a week, for a 5 month period (n=16; 1.9+/-0.4 miles/day). A sedentary control group sat daily on immobile treadmills (n=8). Half of the runners had an additional sedentary period for 3 months at the end of the exercise period (n=8). In all groups, half of the monkeys were middle-aged (10-12 years old) and half were more mature (15-17 years old). Starting the fifth week of exercise training, monkeys underwent cognitive testing using the Wisconsin General Testing Apparatus (WGTA). Regardless of age, the exercising group learned to use the WGTA significantly faster (4.6+/-3.4 days) compared to controls (8.3+/-4.8 days; P=0.05). At the end of 5 months of running monkeys showed increased fitness, and the vascular volume fraction in the motor cortex in mature adult running monkeys was increased significantly compared to controls (P=0.029). However, increased vascular volume did not remain apparent after a 3-month sedentary period. These findings indicate that the level of exercise associated with improved fitness in middle-aged humans is sufficient to increase both the rate of learning and blood flow to the cerebral cortex, at least during the period of regular exercise.

Dispersion and diameter separation of multi-wall carbon nanotubes in aqueous solutions

Comparative studies on dispersing of multi-wall carbon nanotubes (CNTs) using two anionic surfactants (sodium dodecyl sulphate, SDS, and sodium dodecyl benzenosulfonate, SDBS) are presented. The studies were conducted on the surfactant concentrations that were close to the critical micelle concentration (CMC). The stability of CNTs suspensions obtained for surfactant solutions at concentrations lower than the CMC was investigated. It was also found that the surfactant structure has an influence on the diameter distribution of dispersed CNTs.

The exosome and 3'-5' RNA degradation in plants

One of the most versatile RNA degradation machines in eukaryotes is the 3'-5' RNA exosome. It consists of nine conserved subunits forming the core complex, which associates with active ribonucleases, RNA binding proteins, helicases and additional co-factors. While yeast and human exosome core complexes are catalytically inactive, the plant core complex has probably retained a phosphorolytic activity. Intriguingly, the down-regulation of individual subunits of the plant core complex in Arabidopsis mutants led to distinct developmental defects, suggesting an unequal contribution of the core subunits to the in vivo activities of the plant exosome complex. In addition, some of the plant core subunits as well as some associated factors are encoded by duplicated genes, which may have both overlapping and specific functions. Together, these results suggest an unique and complex organisation of exosome-mediated RNA degradation processes in plants. This chapter reviews our current knowledge of plant exosomes and discusses the impact of 3'-5' RNA degradation on the posttranscriptional control of plant genome expression.

Allergen IgE-isotype-specific suppression by maternally derived monoclonal anti-IgG-idiotype

BACKGROUND

The dramatic increase of IgE-mediated allergic diseases in western countries demonstrates the urgent need for new therapeutic or prophylactic approaches. In mice, a prophylactic long-lasting allergen-specific suppression of IgE responsiveness is induced by maternal IgG antibodies to allergens like ovalbumin, phospholipase A(2) (bvPLA(2)) or ovomucoid. As neonatal application or maternally derived pathogen-reactive antibodies (idiotypes) as well as corresponding anti-idiotypes can induce anti-microbial protection, we probed the transgenerational IgE-suppressive mechanism with a syngeneic monoclonal anti-idiotypic antibody.

METHODS

The monoclonal bee-venom-phospholipase A(2) (bvPLA(2))-reactive IgG antibody MS613 (idiotype) or the corresponding syngeneic anti-idiotype II/2-19 were injected during the first 2 days postpartum to the dams. Immunization of offspring with minute doses of IgE-inducing bvPLA(2) was started at an adult age of 3(1/2) months.

RESULTS

The postnatal transfer of the anti-bvPLA(2) idiotype MS613 or the corresponding anti-idiotype II/2-19 induced long-lasting allergen-specific IgE suppression in a dose-dependent manner, while the IgG response to the allergen developed normally. Quantitatively, the anti-idiotype was more effective than idiotype. Molecular modeling of the idiotype-anti-idiotype complex and its comparison with the bvPLA(2) structure revealed that the anti-idiotype does not mimic bvPLA(2) epitopes and thus can not be regarded as an internal image antibody and, consequently, does not function as a surrogate antigen.

CONCLUSIONS

Idiotypic network reactivity is at least one major factor for induction of transgenerational IgE suppression by maternal IgG antibodies. If applicable to humans, these data suggest the possibility of a prophylactic and possibly therapeutic treatment of IgE-mediated allergic diseases with anti-idiotypic antibodies.

Polyadenylation-assisted RNA degradation processes in plants

Polyadenylation is a multifunctional post-transcriptional modification that is best known for stabilizing eukaryotic mRNAs and promoting their translation. However, the primordial role of polyadenylation is to target RNAs for degradation by 3' to 5' exoribonucleases. Polyadenylation-assisted RNA degradation contributes to post-transcriptional control in the three genetic compartments of a plant cell: the nucleus, the chloroplast and the mitochondrion. Here, we review the current knowledge of this RNA degradation pathway in these compartments, highlighting recent results that emphasize the crucial role of polyadenylation-assisted RNA degradation in plant genome expression. We also discuss other possible roles of polyadenylation and its sister process polyuridylation.

Polyadenylation-mediated RNA degradation in plant mitochondria

In plant mitochondria, polyadenylation-mediated RNA degradation is involved in several key aspects of genome expression, including RNA maturation, RNA turnover, and RNA surveillance. We describe here a combination of in vivo, in vitro, and in organello methods that have been developed or optimized to characterize this RNA degradation pathway. These approaches include several PCR-based methods designed to identify polyadenylated RNA substrates, as well as in vitro and in organello systems, to study functional aspects of the RNA degradation processes. Taken together, identification of RNA substrates combined with information from degradation assays are invaluable tools to dissect the mechanisms and roles of RNA degradation in plant mitochondrial genome expression.

Single-walled carbon nanotubes synthesis: a direct comparison of laser ablation and carbon arc routes

Carbon arc and chemical vapor deposition are at present the most efficient methods for mass production of single-walled carbon nanotubes. However, laser ablation is renowned for high quality nanotubes with narrow diameter distributions and hence is also of great interest. The aim of this work was to compare both the carbon arc and laser ablation techniques with respect to the quality--and relative yield of the produced SWCNTs. For this comparative study we used Fe as the catalyst, which is known not to be very active in laser ablation. However, we show this is not the case when H2 is included in the reaction. The reactions for both synthesis routes were carried out in a N2-H2 (95-5% vol.) atmosphere. The same homogenous carbon rods with different iron contents, between 1 and 5 at.% were used as the carbon feedstock and catalyst supply in both synthesis routes. Additionally, two types of carbon rods containing 1 at.% Fe with different graphitization degrees were also investigated. In the arc-discharge case, the low-graphitized electrode produced a web-like product rich in SWCNTs, while the high-graphitized carbon rods yielded soot containing carbon-encapsulated iron nanocrystallites, amorphous carbon nanoparticles, and surprisingly a small fraction of SWCNTs. With laser ablation synthesis, the Fe content and the reactor temperature significantly influenced the SWCNTs yield. Carbon arc plasma diagnostics were also performed. By using optical emission and Absorption spectroscopy the plasma temperature, C2 and CN radical content in the arc zone were determined.