RNA interference tolerates 2'-fluoro modifications at the Argonaute2 cleavage site

Short interfering RNA (siRNA) molecules with good gene-silencing properties are needed for drug development based on RNA interference (RNAi). An initial step in RNAi is the activation of the RNA-induced silencing complex RISC, which requires degradation of the sense strand of the siRNA duplex. Although various chemical modifications have been introduced to the antisense strand, modifications to the Argonaute2 (Ago2) cleavage site in the sense strand have, so far, not been described in detail. In this work, novel 2'-F-purine modifications were introduced to siRNAs, and their biological efficacies were tested in cells stably expressing human tartrate-resistant acid phosphatase (TRACP). A validated siRNA that contains both purine and pyrimidine nucleotides at the putative Ago2 cleavage site was chemically modified to contain all possible combinations of 2'-fluorinated 2'-deoxypurines and/or 2'-deoxypyrimidines in the antisense and/or sense strands. The capacity of 2'-F-modified siRNAs to knock down their target mRNA and protein was studied, together with monitoring siRNA toxicity. All 2'-F-modified siRNAs resulted in target knockdown at nanomolar concentrations, despite their high thermal stability. These experiments provide the first evidence that RISC activation not only allows 2'-F modifications at the sense-strand cleavage site, but also increase the biological efficacy of modified siRNAs in vitro.     

Transformation of nuclear and plastomic plant genomes by biolistic particle bombardment

Microprojectile bombardment is a powerful method for the transformation of various organisms and tissues. For plants, the biolistic approach is primarily used for transformation of cereals and other monocotyledons, as well as for dicotyledonous plants shown to be recalcitrant to Agrobacterium-based transformation of organellar genomes, and transformation of plant and algal chloroplasts has recently been reported. In this protocol paper we provide methods for nuclear and plastomic transformation of plants using the biolistic technique.     

The dibenzodioxocin lignin substructure is abundant in the inner part of the secondary wall in Norway spruce and silver birch xylem

A specific condensed lignin substructure, dibenzodioxocin, was immunolocalized in differentiating cell walls of Norway spruce (Picea abies (L.) H. Karsten) and silver birch (Betula pendula Roth) xylem. A fluorescent probe, Alexa 488 was used as a marker on the dibenzodioxocin-specific secondary antibody. For the detection of this lignin substructure, 25-m cross-sections of xylem were viewed with a confocal laser-scanning microscope with fluorescein isothiocyanate fluorescence filters. In mature cells, fluorescence was detected in the S3 layer of the secondary wall in both tree species, but it was more intense in Norway spruce than in silver birch. In silver birch most of the signal was detected in vessel walls and less in fiber cell walls. In very young tracheids of Norway spruce and vessels and fibers of silver birch, where secondary cell wall layers were not yet formed, the presence of the dibenzodioxocin structure could not be shown.Abbreviation CLSM confocal laser-scanning fluorescence microscopy     

Reinnervation of arterial grafts by adrenergic nerves occurs in rats as indicated by increased levels of noradrenaline

To investigate the changes in noradrenaline concentrations in transplanted arterial grafts in rats, 31 female rats 4 to 6 weeks old of the AO/Ks:OC strain were operated on. Femoral arterial grafts were anastomosed to carotid arteries and compared with control femoral segments. Six rats were included in each follow-up group at 0, 1, 4, and 12 weeks, and there were seven rats in the 20-week follow-up group. High-performance liquid chromatography was used to determine the concentrations of noradrenaline. The operation itself decreased noradrenaline concentrations in the grafts to 76 percent of that in the control segments. One week after the operation, the noradrenaline concentration had fallen to 1.7 percent of the control values and started to recover thereafter. One month after the operation, it was 23 percent; at 3 months, it was 31 percent; and at 5 months, it was 43 percent of control values. The decrease from time 0 to 1 week was significant (p = 0.001), as was the increase from 1 week to 20 weeks (p = 0.004). Noradrenaline concentrations had fallen significantly 1 week after the operation and thereafter they increased to levels comparable to those seen in the immediate postoperative period.     

The structure of bovine lysosomal alpha-mannosidase suggests a novel mechanism for low-pH activation

Lysosomal alpha-mannosidase (LAM: EC 3.2.1.24) belongs to the sequence-based glycoside hydrolase family 38 (GH38). Two other mammalian GH38 members, Golgi alpha-mannosidase II (GIIAM) and cytosolic alpha-mannosidase, are expressed in all tissues. In humans, cattle, cat and guinea pig, lack of lysosomal alpha-mannosidase activity causes the autosomal recessive disease alpha-mannosidosis. Here, we describe the three-dimensional structure of bovine lysosomal alpha-mannosidase (bLAM) at 2.7A resolution and confirm the solution state dimer by electron microscopy. We present the first structure of a mammalian GH38 enzyme that offers indications for the signal areas for mannose phosphorylation, suggests a previously undetected mechanism of low-pH activation and provides a template for further biochemical studies of the family 38 glycoside hydrolases as well as lysosomal transport. Furthermore, it provides a basis for understanding the human form of alpha-mannosidosis at the atomic level. The atomic coordinates and structure factors have been deposited in the Protein Data Bank (accession codes 1o7d and r1o7dsf).     

Tartrate-resistant acid phosphatase 5B circulates in human serum in complex with alpha2-macroglobulin and calcium

Tartrate-resistant acid phosphatase (TRACP) is an enzyme with unknown biological function. In addition to its acid phosphatase activity, TRACP is capable of generating reactive oxygen species (ROS) at neutral pH. Two forms of TRACP circulate in human serum, macrophage-derived TRACP 5a and osteoclast-derived TRACP 5b. Here we have studied the circulating forms of the osteoclast-derived TRACP 5b in rat and human serum. In human serum, TRACP 5b circulates in a large complex that contained α₂M and calcium. On the contrary, rat serum TRACP 5b circulates as a free molecule. Formation of the TRACP 5b complex in vitro decreased significantly the ROS generating activity of TRACP 5b without affecting its phosphatase activity. These results suggest that the complex formation may be necessary to eliminate the formation of the harmful ROS in the neutral pH of serum.     

Multilevel phenotypic selection on morphological characters in a metapopulation of Silene tatarica

This study partitions selection in a natural metapopulation of a riparian plant species, Silene tatarica, into individual- and patch-level components by using contextual analysis, in which a patch refers to a spatially distinct stand of individual plants. We estimated selection gradients for two morphological characters (plant height and number of stems), their respective patch means, and plant density with respect to reproductive success in a two-year study. The approach was also extended to partition selection separately within habitats with varying degrees of exposure to river disturbances and herbivory. The selection differentials and gradients for plant height were positive at both individual and patch levels, with selection forces highest in the closed habitat with low exposure to disturbance. This pattern suggests that local groups with taller than average plants are more visible to pollinators than to groups that are shorter than average plants; and, within patches, individuals with short stature are visited less often than taller ones. Selection on the number of stems was in opposition at individual and patch levels. At the individual level the character was selected toward higher values, whereas selection at the patch-level favored smaller mean number of stems. The strength of the latter component was associated with the intensity of herbivory in different habitats, suggesting that the patch-level selection against a large number of stems might be due to high attractiveness of such patches to the main herbivore, reindeer. Consequently, direction and strength of selection in spatially structured populations may depend significantly on fitness effects arising at the group level.     

Enhanced production of Trichoderma reesei endoglucanases and use of the new cellulase preparations in producing the stonewashed effect on denim fabric

Trichoderma reesei strains were constructed for production of elevated amounts of endoglucanase II (EGII) with or without cellobiohydrolase I (CBHI). The endoglucanase activity produced by the EGII transformants correlated with the copy number of the egl2 expression cassette. One copy of the egl2 expression cassette in which the egl2 was under the cbh1 promoter increased production of endoglucanase activity 2.3-fold, and two copies increased production about 3-fold above that of the parent strain. When the enzyme with elevated EGII content was used, an improved stonewashing effect on denim fabric was achieved. A T. reesei strain producing high amounts of EGI and -II activities without CBHI and -II was constructed by replacing the cbh2 locus with the coding region of the egl2 gene in the EGI-overproducing CBHI-negative strain. Production of endoglucanase activity by the EG-transformant strain was increased fourfold above that of the host strain. The filter paper-degrading activity of the endoglucanase-overproducing strain was lowered to below detection, presumably because of the lack of cellobiohydrolases.     

Localization of dibenzodioxocin substructures in lignifying Norway spruce xylem by transmission electron microscopy–immunogold labeling

The lignification process in mature Norway spruce [Picea abies (L.) H. Karsten] xylem cell walls was studied using transmission electron microscopy (TEM)–immunogold detection with a polyclonal antibody raised against a specific lignin substructure, dibenzodioxocin. The study reveals for the first time the exact location of this abundant eight-ring structure in the cell wall layers of wood. Spruce wood samples were collected in Southern Finland at the time of active growth and lignification of the xylem cell walls. In very young tracheids where secondary cell wall layers were not yet formed, the presence of the dibenzodioxocin structure could not be shown at all. During secondary cell wall thickening, the dibenzodioxocin structure was more abundant in the secondary cell wall layers than in the middle lamella. The highest number of gold particles revealing dibenzodioxocin was in the S2+S3 layer. Statistically significant differences were found in the frequency of gold particles present in various cell wall layers. For comparison, wood sections were also cut with a cryomicrotome for light and fluorescence microscopy.     

High-yield production of a bacterial xylanase in the filamentous fungus Trichoderma reesei requires a carrier polypeptide with an intact domain structure

A bacterial xylanase gene, Nonomuraea flexuosa xyn11A, was expressed in the filamentous fungus Trichoderma reesei from the strong cellobiohydrolase 1 promoter as fusions to a variety of carrier polypeptides. By using single-copy isogenic transformants, it was shown that production of this xylanase was clearly increased (up to 820 mg/liter) when it was produced as a fusion protein with a carrier polypeptide having an intact domain structure compared to the production (150 to 300 mg/liter) of fusions to the signal sequence alone or to carriers having incomplete domain structures. The carriers tested were the T. reesei mannanase I (Man5A, or MANI) core-hinge and a fragment thereof and the cellulose binding domain of T. reesei cellobiohydrolase II (Cel6A, or CBHII) with and without the hinge region(s) and a fragment thereof. The flexible hinge region was shown to have a positive effect on both the production of Xyn11A and the efficiency of cleavage of the fusion polypeptide. The recombinant Xyn11A produced had properties similar to those of the native xylanase. It constituted 6 to 10% of the total proteins secreted by the transformants. About three times more of the Man5A core-hinge carrier polypeptide than of the recombinant Xyn11A was observed. Even in the best Xyn11A producers, the levels of the fusion mRNAs were only approximately 10% of the level of cel7A (cbh1) mRNA in the untransformed host strain.