Specific Binding of the Pathogenic Prion Isoform: Development and Characterization of a Humanized Single-Chain Variable Antibody Fragment

Murine monoclonal antibody V5B2 which specifically recognizes the pathogenic form of the prion protein represents a potentially valuable tool in diagnostics or therapy of prion diseases. As murine antibodies elicit immune response in human, only modified forms can be used for therapeutic applications. We humanized a single-chain V5B2 antibody using variable domain resurfacing approach guided by computer modelling. Design based on sequence alignments and computer modelling resulted in a humanized version bearing 13 mutations compared to initial murine scFv. The humanized scFv was expressed in a dedicated bacterial system and purified by metal-affinity chromatography. Unaltered binding affinity to the original antigen was demonstrated by ELISA and maintained binding specificity was proved by Western blotting and immunohistochemistry. Since monoclonal antibodies against prion protein can antagonize prion propagation, humanized scFv specific for the pathogenic form of the prion protein might become a potential therapeutic reagent

Translational Selection Is Ubiquitous in Prokaryotes

Codon usage bias in prokaryotic genomes is largely a consequence of background substitution patterns in DNA, but highly expressed genes may show a preference towards codons that enable more efficient and/or accurate translation. We introduce a novel approach based on supervised machine learning that detects effects of translational selection on genes, while controlling for local variation in nucleotide substitution patterns represented as sequence composition of intergenic DNA. A cornerstone of our method is a Random Forest classifier that outperformed previous distance measure-based approaches, such as the codon adaptation index, in the task of discerning the (highly expressed) ribosomal protein genes by their codon frequencies. Unlike previous reports, we show evidence that translational selection in prokaryotes is practically universal: in 460 of 461 examined microbial genomes, we find that a subset of genes shows a higher codon usage similarity to the ribosomal proteins than would be expected from the local sequence composition. These genes constitute a substantial part of the genome—between 5% and 33%, depending on genome size—while also exhibiting higher experimentally measured mRNA abundances and tending toward codons that match tRNA anticodons by canonical base pairing. Certain gene functional categories are generally enriched with, or depleted of codon-optimized genes, the trends of enrichment/depletion being conserved between Archaea and Bacteria. Prominent exceptions from these trends might indicate genes with alternative physiological roles; we speculate on specific examples related to detoxication of oxygen radicals and ammonia and to possible misannotations of asparaginyl–tRNA synthetases. Since the presence of codon optimizations on genes is a valid proxy for expression levels in fully sequenced genomes, we provide an example of an “adaptome” by highlighting gene functions with expression levels elevated specifically in thermophilic Bacteria and Archaea

Meningiomas exhibit loss of heterozygosity of the APC gene

The molecular mechanisms and candidate genes involved in development of meningiomas still need investigation and elucidation. In the present study 33 meningiomas were analyzed regarding genetic changes of tumor suppressor gene Adenomatous polyposis coli (APC), a component of the wnt signaling. Gene instability was tested by polymerase chain reaction/loss of heterozygosity (LOH) using Restriction Fragment Length Polymorphism (RFLP) method. RFLP was performed by two genetic markers, Rsa I in APC's exon 11 and Msp I in its exon 15. The results of our analysis showed altogether 15 samples with LOH of the APC gene out of 32 heterozygous patients (47%). Seven patients had LOHs at both exons, while four LOHs were exclusive for exon 11 and four for exon 15. The changes were distributed according to pathohistological grade as follows: 46% of meningothelial meningioma showed LOH; 33% of fibrous; 75% of mixed (transitional); 75% of angiomatous, and one LOH was found in a single case of psammomatous meningioma. None of the LOHs were found in atypical and anaplastic cases. Immunostaining showed that samples with LOHs were accompanied with the absence of APC protein expression or presence of mutant APC proteins (chi(2 )= 13.81, df = 2, P < 0.001). We also showed that nuclear localization of beta-catenin correlates to APC genetic changes (chi(2 )= 21.96, df = 2, P < 0.0001). The results of this investigation suggest that genetic changes of APC gene play a role in meningioma formation

Survival and Recovery Following Wildfire in the Southern Range of the Coast Redwood Forest

Fire plays a central role in determining structure, composition, and recruitment in many forest types. In coast redwood forests, the role of fire is not well understood and scant literature exists on post-fire response, particularly in the southern part of the range. In order to better understand patterns of survival and recruitment following fire for coast redwood (Sequoia sempervirens [lamb. ex D. Don] Endl.) and associated tree species, three sites in the Santa Cruz Mountains, California, USA, were sampled following wildfire. Randomly selected 10 m diameter plots were used to collect data on survivorship and post fire regeneration in order to analyze short-term responses including mortality, crown retention, basal sprouting, canopy regeneration, and seedling production. Results indicated that coast redwood had the lowest percent mortality (11.98 %) and highest mean canopy retention (43.10 %) of all species sampled, followed by Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) (25.54 %), tanoak (Notholithocarpus densiflorus [Hook. & Arn.] Manos) (23.27 %), combined oak species (Quercus sp.) (6.67 %), and Pacific madrone (Arbutus menziesii Pursh) (4.13 %). In addition, associated species experienced higher survival rates when proximate to coast redwoods. Coast redwood trees also exhibited the highest canopy regeneration (53 %), the highest average density of basal sprouts (3.54 × 104 ha), and the greatest average number of seedlings, ranging from zero to 2.09 × 105seedlings ha-1. Overall, coast redwood appeared to have a balance of fire adaptive features, exceeding all associated species, which allow individual trees to withstand fire, while at the same time promoting recruitment following fire