Comparison of basic peptides- and lipid-based strategies for the delivery of splice correcting oligonucleotides

Expression of alternatively spliced mRNA variants at specific stages of development or in specific cells and tissues contributes to the functional diversity of the human genome. Aberrations in alternative splicing were found as a cause or a contributing factor to the development, progression, or maintenance of numerous diseases. The use of antisense oligonucleotides (ON) to modify aberrant expression patterns of alternatively spliced mRNAs is a novel means of potentially controlling such diseases. Oligonucleotides can be designed to repair genetic mutations, to modify genomic sequences in order to compensate for gene deletions, or to modify RNA processing in order to improve the effects of the underlying gene mutation. Steric block ON approach have proven to be effective in experimental model for various diseases. Here, we describe our experience in investigating two strategies for ON delivery: ON conjugation with basic peptides and lipid-based particulate system (lipoplex). Basic peptides or Cell Penetrating Peptides (CPP) such as the TAT-derived peptide appear to circumvent many problems associated with ON and drug delivery. This strategy may represent the next paradigm in our ability to modulate cell function and offers a unique avenue for the treatment of disease. Lipoplexes result from the intimate interaction of ON with cationic lipids leading to ON carrying particles able to be taken up by cells and to release ON in the cytoplasm. We have used as an experimental model the correction of a splicing alteration of the mutated β-globin intron causing thalassemia. Data on cell penetration and efficacy of correction of specific steric block ON delivered either by basic peptides or lipoplex are described. A comparison of the properties of both delivery systems is made respective to the use of this new class of therapeutic molecules.     

时间序列修订对森林二氧化碳通量的影响

对长白山阔叶红松林2003年生长季的涡动相关实测时间序列进行了去倾修订与超声风速仪倾斜修订,并分析了不同修订方法对森林CO2通量计算值的影响．结果表明,基于未修订时间序列计算得到的森林CO2通量(Fcraw)被高估．线性与非线性去倾对Fcraw的修订量分别为1．6％、1．8％,两者差异很小．平面拟合坐标变换与流线坐标变换对Fcraw的修订量分别为3．7％、4．7％,两者差异较大．对线性去倾后的时间序列分别进行流线坐标变换与平面拟合坐标变换,二者对Fcraw的修订量分别为5．5％与4．6％．建议对时间序列进行线性去倾与平面拟合坐标变换综合修订．     

Two human valyl-tRNA synthetase-encoding cDNA sequences deposited in GenBank display extensive differences

Five blocks of significant differences exist between two published sequences of the cDNA encoding human valyl-tRNA synthetase (GenBank X59303 and M98326). By comparison with the partial sequence of rat valyl-tRNA synthetase (GenBank M98327) the correct sequence can be deduced for two such blocks. The possible origin of the diversity for the two sequences is discussed.     

The pentafunctional FAS1 genes of Saccharomyces cerevisiae and Yarrowia lipolytica are co-linear and considerably longer than previously estimated

Summary The fatty acid synthetase (FAS) gene FAS1 of the alkane-utilizing yeast Yarrowia lipolytica was cloned and sequenced. The gene is represented by an intron-free reading frame of 6228 by encoding a protein of 2076 amino acids and 229980 Da molecular weight. This protein exhibits a 58% sequence similarity to the corresponding Saccharomyces cerevisiae FAS -subunit. The sequential order of the five FAS1-encoded enzyme domains, acetyl transferase, enoyl reductase, dehydratase and malonyl/palmityl-transferase, is co-linear in both organisms. This finding agrees with available evidence that the functional organization of FAS genes is similar in related organisms but differs considerably between unrelated species. In addition, previously reported conflicting data concerning the 3 end of S. cerevisiae FAS1 were re-examined by genomic and cDNA sequencing of the relevant portion of the gene. Thereby, the translational stop codon was shown to lie considerably downstream of both published termination sites. The S. cerevisiae FAS1 gene thus has a corrected length of 6153 by and encodes a protein of 2051 amino acids and 228667 Da molecular weight.     

Case-control and case-only designs with genotype and family history data: estimating relative risk, residual familial aggregation, and cumulative risk

In case-control studies of inherited diseases, participating subjects (probands) are often interviewed to collect detailed data about disease history and age-at-onset information in their family members. Genotype data are typically collected from the probands, but not from their relatives. In this article, we introduce an approach that combines case-control analysis of data on the probands with kin-cohort analysis of disease history data on relatives. Assuming a marginally specified multivariate survival model for joint risk of disease among family members, we describe methods for estimating relative risk, cumulative risk, and residual familial aggregation. We also describe a variation of the methodology that can be used for kin-cohort analysis of the family history data from a sample of genotyped cases only. We perform simulation studies to assess performance of the proposed methodologies with correct and mis-specified models for familial aggregation. We illustrate the proposed methodologies by estimating the risk of breast cancer from BRCA1/2 mutations using data from the Washington Ashkenazi Study.     

Pollux: platform independent error correction of single and mixed genomes

Background

Second-generation sequencers generate millions of relatively short, but error-prone, reads. These errors make sequence assembly and other downstream projects more challenging. Correcting these errors improves the quality of assemblies and projects which benefit from error-free reads.

Results

We have developed a general-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and correct insertion, deletion, and homopolymer errors while remaining sensitive to low coverage areas of sequencing projects. Using published data sets, we correct 94% of Illumina MiSeq errors, 88% of Ion Torrent PGM errors, 85% of Roche 454 GS Junior errors. Introduced errors are 20 to 70 times more rare than successfully corrected errors. Furthermore, we show that the quality of assemblies improves when reads are corrected by our software.

Conclusions

Pollux is highly effective at correcting errors across platforms, and is consistently able to perform as well or better than currently available error correction software. Pollux provides general-purpose error correction and may be used in applications with or without assembly.     

Gafchromic film dosimetry: Four years experience using FilmQA Pro software and Epson flatbed scanners

Purposes: To assess performance of FilmQA Pro software for pre-treatment patient-specific quality assurance (QA), using radiochromic films and two commercial flatbed scanners. To evaluate a novel multichannel approach compared to the classical red channel evaluation.Material and methodsPatient films (mostly EBT2 films, one box of EBT3) were digitalized using successively two flatbed scanners: the A4-size Epson V750 and the A3-size Epson 10000XL. Prior to patient dose verification, basic characteristics of films and scanners were investigated. Patient films were analyzed using FilmQA Pro software, which enables to use the signal from all three colour channels (Red, Green, Blue).ResultsCompared to the red channel evaluation, multichannel evaluation presents better passing rates with regard to local gamma index. As expected, we obtained better results using A3-size scanner compared to A4-size scanner, especially when considering large region of interest. An observation of great interest was made for both scanners: after intensive use, a tilting in the blue transmittance profiles appeared in the lamp direction, making multichannel analysis unsuitable for accurate dose evaluation.     

Key taste components in two wild edible Boletus mushrooms using widely targeted metabolomics

Compounds from wild edible mushrooms has been reported to exert biological activities and contribute to the different flavors of mushrooms in our diet. Wild edible Boletus mushrooms are popular in Southwest China. In this study, we performed ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS) based on widely targeted metabolomics analysis to identify key components. A total of 194 metabolites (113 upregulated, 81 downregulated) divided into 11 groups (49 metabolites in group lipids, 34 in amino acids and derivatives, 30 in organic acids, 18 in phenolic acids, 16 in nucleotides and derivatives, 13 in alkaloids, 6 in flavonoids, 3 in lignans and coumarins, 3 in tannins, 2 in terpenoids, and 20 in others) were found among Boletus bainiugan compared with B. subsplendidus. Through clustering analysis, principal component analysis (PCA), and orthogonal signal correction and partial least squares-discriminant analysis (OPLS-DA), different metabolites from fruiting bodies were clearly identified. Significant differences were observed in the metabolites between Boletus bainiugan and B. subsplendidus. These metabolites are involved in important biological functions. Our results provide new insights into important metabolites and theoretical basis for the taste difference of two wild edible Boletus mushrooms.