Targeting RNA for Degradation with a (2′, 5′)-Oligoadenylate Antisense Chimera

Abstract

A novel method is described to selectively cleave RNA by harnessing the 2-5A-dependent ribonuclease.     

Seed Rain in Natural Grassland and Adjacent Ski Run in the Swiss Alps: A Preliminary Report

Seed rain was studied during one growing season in an intact high-alpine grassland and in a downhill ski run that had been machine-graded about 26 years earlier. The study plots were located at about 2500 meters above sea level. The number of trapped seeds per square meter in the grassland was significantly larger than in the ski run (930 versus 96, respectively). Alpha diversity in seed rain was about two times higher in the grassland than in the ski run. Seed rain was primarily influenced by site conditions but also varied in space and time, and both the actual number of diaspores and the species composition changed throughout the growing season. Most of the species found in the seed rain occurred in the standing vegetation, but some clearly arrived from outside. Seed rain in both sites was dominated by a few species, and no clear relationships were found between the species abundance in standing vegetation and in the seed rain. The results of this preliminary study contribute to a better understanding of plant behavior in high-alpine sites and will be helpful in planning and implementing restoration work above the timberline.     

Die Ausnutzung des Zooplanktons durch planktonfressende Fische in Abhängigkeit von abiotischen Faktoren im Oderhaff

Zusammenfassung 1. In den Jahren 1955–1958 wurden im Oderhaff Untersuchungen durchgeführt über die quantitative Dynamik zwischen Artzusammensetzung und Quantität des Zooplanktons einerseits und Wachstum und Nahrungsaufnahme planktonfressender Fische andererseits.2. Die jahreszeitlich bedingten Veränderungen in der Planktonzusammensetzung üben einen starken quantitativen und qualitativen Einfluß aus auf die Nahrungszusammensetzung planktonfressender Fische (Mageninhaltsuntersuchungen).3. Die pro Zeiteinheit aufgenommene Nahrungsmenge ist in starkem Maße von der Quantität des zur Verfügung stehenden Zooplanktons abhängig.4. Die Dynamik der Beziehungen Fischfraß — Zooplankton und Zooplankton — Fischfraß ist eng verbunden mit jahreszeitlichen Fluktuationen der abiotischen Umweltfaktoren.5. Futterreichtum bewirkt eine Erhöhung des Zuwachstempos und des Futterverwertungskoeffizienten der Fische.6. Fischarten, deren Nahrung nicht ausschließlich aus Zooplankton besteht, erschließen sich in Zeiten mit geringer Zooplanktonbiomasse andere Nahrungsquellen und andere Futterplätze.7. Der Einfluß des Fischfraßes auf die Bildung und Vermehrung der Zooplanktongemeinschaften ist schwer zu beurteilen. Er läßt sich aber nachweisen, und zwar vor allem in Perioden mit herabgesetzter Reproduktionskapazität der Planktonorganismen und mit gesteigertem Nahrungskonsum der Fische. Es wurden zwei solche Perioden pro Jahr im Oderhaff festgestellt.

---

The utilization of zooplankton by plankton-eating fishes in relation to abiotic factors in the Szczecin Gulf

The investigations were carried out in the middle area of the Szczecin Gulf, Poland, from 1955 to 1958. The seasonal and year-by-year fluctuations in the quality and quantity of zooplankton stocks may cause parallel changes in the food uptake of plankton-eating fishes. In fishes feeding primarily on zooplankton, changes were found in stomach contents, daily food consumption, efficiency of food utilization and growth rate. Fishes feeding only temporarily on zooplankton either increase their consumption of other food organisms as the zooplankton biomass decreases (2-year-oldOsmerus eperlanus andLucioperca lucioperca) or look for new feeding grounds (young ofAcerina cernua andAbramis brama). In order to analyse the effects of fish predation on the zooplankton biomass, the following phenomena were investigated: (a) annual fluctuations of fish predations (mainlyO. eperlanus); (b) annual fluctuations in reproduction patterns of Cladocera species of importance as fish food(Daphnia hyalina, D. cuculata) relative to changes in the abiotic environment; (c) annual fluctuations in total mortality of the twoDaphnia species mentioned. During the reproductive period the rate of reproduction inDaphnia is always higher than the maximum increase in daily food requirements of the growingO. eperlanus. Fish predation may represent a severe stress for theDaphnia populations during two periods per year. In these periods the situation is characterized by (a) decrease of prey reproduction rate and increase in daily food requirements of the growingO. eperlanus; (b) faster decrease of prey reproduction rate relative to a parallel decrease in food requirements of the predator.

     

Blockade of CXCR3 receptor:ligand interactions reduces leukocyte recruitment to the lung and the severity of experimental idiopathic pneumonia syndrome

Idiopathic pneumonia syndrome (IPS) is a frequently fatal complication after allogeneic stem cell transplantation (allo-SCT) that responds poorly to standard immunosuppressive therapy. The pathophysiology of IPS involves the secretion of inflammatory cytokines including IFN-gamma and TNF-alpha along with the recruitment of donor T cells to the lung. CXCR3 is a chemokine receptor that is expressed on activated Th1/Tc1 T cell subsets and the expression of its ligands CXCL9 (monokine induced by IFN-gamma (Mig)) and CXCL10 (IFN-gamma-inducible protein 10 (IP-10)) can be induced in a variety of cell types by IFN-gamma alone or in combination with TNF-alpha. We used a lethally irradiated murine SCT model (B6 --> bm1) to evaluate the role of CXCR3 receptor:ligand interactions in the development of IPS. We found that Mig and IP-10 protein levels were significantly elevated in the bronchoalveolar lavage fluid of allo-SCT recipients compared with syngeneic controls and correlated with the infiltration of IFN-gamma-secreting CXCR3(+) donor T cells into the lung. The in vivo neutralization of either Mig or IP-10 significantly reduced the severity of IPS compared with control-treated animals, and an additive effect was observed when both ligands were blocked simultaneously. Complementary experiments using CXCR3(-/-) mice as SCT donors also resulted in a significant decrease in IPS. These data demonstrate that interactions involving CXCR3 and its primary ligands Mig and IP-10 significantly contribute to donor T cell recruitment to the lung after allo-SCT. Therefore, approaches focusing on the abrogation of these interactions may prove successful in preventing or treating lung injury that occurs in this setting.     

A regulatory role for NBS1 in strand-specific mutagenesis during somatic hypermutation

Activation-induced cytidine deaminase (AID) is believed to initiate somatic hypermutation (SHM) by deamination of deoxycytidines to deoxyuridines within the immunoglobulin variable regions genes. The deaminated bases can subsequently be replicated over, processed by base excision repair or mismatch repair, leading to introduction of different types of point mutations (G/C transitions, G/C transversions and A/T mutations). It is evident that the base excision repair pathway is largely dependent on uracil-DNA glycosylase (UNG) through its uracil excision activity. It is not known, however, which endonuclease acts in the step immediately downstream of UNG, i.e. that cleaves at the abasic sites generated by the latter. Two candidates have been proposed, an apurinic/apyrimidinic endonuclease (APE) and the Mre11-Rad50-NBS1 complex. The latter is intriguing as this might explain how the mutagenic pathway is primed during SHM. We have investigated the latter possibility by studying the in vivo SHM pattern in B cells from ataxia-telangiectasia-like disorder (Mre11 deficient) and Nijmegen breakage syndrome (NBS1 deficient) patients. Our results show that, although the pattern of mutations in the variable heavy chain (V(H)) genes was altered in NBS1 deficient patients, with a significantly increased number of G (but not C) transversions occurring in the SHM and/or AID targeting hotspots, the general pattern of mutations in the V(H) genes in Mre11 deficient patients was only slightly altered, with an increased frequency of A to C transversions. The Mre11-Rad50-NBS1 complex is thus unlikely to be the major nuclease involved in cleavage of the abasic sites during SHM, whereas NBS1 might have a specific role in regulating the strand-biased repair during phase Ib mutagenesis.     

Geographical patterns of nucleotide diversity and population differentiation in three closely related European pine species in the Pinus mugo complex

Nucleotide polymorphism at 12 nuclear loci and two mitochondrial gene fragments was studied in three closely related pine species from the Pinus mugo complex in populations across the species distributional range in Europe. Despite large differences in the census sizes of the populations, high and similar levels of nucleotide diversity (θ_sil = ～0.013–0.017) were found at nuclear loci in the three pine species. More rapid decay of overall linkage disequilibrium (LD) and recombination to diversity ratio (ρ/θ) was observed across the species distributional range in P. mugo (ρ = 0.0369 ± 0.0028; ρ/θ = ～2.2) than in P. uncinata (ρ = 0.0054 ± 0.0011; ρ/θ = ～0.4) and P. uliginosa (ρ = 0.0051 ± 0.0010, ρ/θ = ～0.4). However, regional groups of P. mugo showed similar levels of LD and ρ/θ ratio to the other species. An excess of rare nucleotide variants was found in P. mugo at four loci, but, overall, the allelic frequency spectrum in the three species did not deviate significantly from neutrality (multilocus Tajima's D = ?0.681, D = ?0.118 and D = ?0.266, P > 0.05, respectively). Bayesian clustering methods showed no clear correspondence of clusters to species or geographical regions. Some differences between populations and species were found in a hierarchical analysis of molecular variance (AMOVA) and in the distribution of the mitochondrial DNA haplotypes, suggesting rather limited gene flow between the taxa and ongoing divergence. As all three pine taxa have similar genetic backgrounds, they form an excellent system for searching for loci involved in adaptive variation and speciation. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 225–238.     

Influence of Drug Binding on DNA Flexibility: A Normal Mode Analysis

Abstract

DNA-drug complexes are important because of their pharmacological interest but, in addition, they provide a useful model to study the essential aspects of DNA recognition processes. In order to investigate the influence of ligand binding on the dynamic properties of DNA we have carried out normal mode analysis for complexes with drugs of two types: a typical intercalator, 9-aminoacridine, and a typical groove binder, netropsin. Normal modes are analysed in terms of helicoidal parameter variations with special attention being paid to global deformations of the double helix. The results show that the influence of these two drugs is very different. Intercalation of 9-aminoacridine leads to an increase in the flexibility of the intercalated dinucleotide step, with notably larger vibrational amplitudes for both roll and twist parameters compared to free DNA. In contrast, the groove binding of netropsin induces a stiffening of the DNA segment which is in contact with the drug reflected by decreased vibrational amplitudes for backbone angles and inter base pair helicoidal parameters and an increase in vibrations for adjacent base pairs in terms of buckle and propeller twist.     

Melatonin concentrations in patients with large goiter before and after surgery

OBJECTIVES: Surgical removal of a very large goiter may traumatize adjacent anatomical structures. The manipulations that involve superior cervical ganglia may alter melatonin secretion. To test this hypothesis we decided to study diurnal serum melatonin profiles in patients with a very large goiter before and after the surgery. MATERIAL AND METHODS:The study was performed on 10 women (mean age-46.5+/-1.6 years; mean+/-SEM; range 39-54 years) with very large non-toxic nodular goiter (mean thyroid volume-125.8+/-25.9 cm (3); mean+/-SEM; range 82.6-326.7 cm(3)). Diurnal serum melatonin profiles were estimated two days before the operation and 10 days after the surgery. Blood samples were collected at 08:00, 12:00, 16:00, 20:00, 22:00, 24:00, 02:00, 04:00, 06:00 and 08:00 h. Melatonin concentration was measured using RIA kit. RESULTS: Nocturnal serum melatonin concentrations (at 24, 02, and 04 hours) were significantly higher after the surgery than before the operation. CONCLUSIONS: Very large goiter may compress the superior cervical ganglia altering indirectly the melatonin synthesis. It cannot be excluded, however, that the presence of the large goiter in some other way affects melatonin secretion.     

Further evidence from sectioned material in support of the existence of a linear terminal complex in cellulose synthesis

Summary Transmembrane linear terminal complexes considered to be involved in the synthesis of cellulose microfibrils have been described in the plasma membrane ofBoergesenia forbesii. Evidence for the existence of these structures has been obtained almost exlusively using the freeze etching technique. In the present study an attempt has been made to complete these studies using conventional fixation, staining, and sectioning procedures. In developing cells ofBoergesenia forbesii, strongly stained structures traversing the plasma membrane and averaging 598.9 nm ± 171.3 nm in length, 28.7 nm ± 4.2 nm in width, and 35.2 nm ± 6.6 nm in depth have been demonstrated. These structures are considered to be linear terminal complexes. At their distal (cell wall) surface, they appear to be closely associated with cellulose microfibrils. At the proximal (cytoplasmic) surface, they are associated with microtubules and polysomes. A model of the possible interrelation of the terminal complexes and microtubules leading to the generation of cell wall microfibrils is proposed.