Recombinase-mediated cassette exchange (RMCE): traditional concepts and current challenges

Traditional DNA transduction routes used for the modification of cellular genomes are subject to unpredictable alterations, as the cell-intrinsic repair machinery may affect both the integrity of the transgene and the recipient locus. These problems are overcome by recombinase-mediated cassette exchange (RMCE) approaches enabling predictable expression patterns by the nondisruptive insertion of a gene cassette at a pre-characterized genomic locus. The destination is marked by a “tag” consisting of two heterospecific recombination target sites (RTs) at the flanks of a selection marker. Provided on a circular donor vector, an analogous cassette encoding the gene of interest can cleanly replace the resident cassette under the influence of a site-specific recombinase. RMCE was first based on the yeast integrase Flp but had to give way to the originally more active phage-derived Cre enzyme. To be effective, both Tyr-recombinases have to be applied at a considerable concentration, which, in the case of Cre, triggers endonucleolytic activities and therefore cellular toxicity. This review addresses the particularities of both recombination routes depending on the structure of the synaptic complex and on improved integrase and RT variants. While the performance of Flp-RMCE can now firmly rely on optimized Flp variants and multiple sets of functional target sites (FRTs), the Cre system suffers from the promiscuity of its RT mutants, which is explained in molecular terms. At present, RMCE enters applications in the stem cell field. Remarkable efforts are noted in the framework of various mouse mutagenesis programs, which, in their first phase, have targeted virtually all genes and now start to shift their emphasis from gene trapping to gene modification.     

The contribution of surface residues to membrane binding and ligand transfer by the α-tocopherol transfer protein (α-TTP)

Previous work has shown that the α-tocopherol transfer protein (α-TTP) can bind to vesicular or immobilized phospholipid membranes. Revealing the molecular mechanisms by which α-TTP associates with membranes is thought to be critical to understanding its function and role in the secretion of tocopherol from hepatocytes into the circulation. Calculations presented in the Orientations of Proteins in Membranes database have provided a testable model for the spatial arrangement of α-TTP and other CRAL-TRIO family proteins with respect to the lipid bilayer. These calculations predicted that a hydrophobic surface mediates the interaction of α-TTP with lipid membranes. To test the validity of these predictions, we used site-directed mutagenesis and examined the substituted mutants with regard to intermembrane ligand transfer, association with lipid layers and biological activity in cultured hepatocytes. Substitution of residues in helices A8 (F165A and F169A) and A10 (I202A, V206A and M209A) decreased the rate of intermembrane ligand transfer as well as protein adsorption to phospholipid bilayers. The largest impairment was observed upon mutation of residues that are predicted to be fully immersed in the lipid bilayer in both apo (open) and holo (closed) conformations such as Phe165 and Phe169. Mutation F169A, and especially F169D, significantly impaired α-TTP-assisted secretion of α-tocopherol outside cultured hepatocytes. Mutation of selected basic residues (R192H, K211A, and K217A) had little effect on transfer rates, indicating no significant involvement of nonspecific electrostatic interactions with membranes.     

Pore‐network modeling of biofilm evolution in porous media

The influence of bacterial biomass on hydraulic properties of porous media (bioclogging) has been explored as a viable means for optimizing subsurface bioremediation and microbial enhanced oil recovery. In this study, we present a pore network simulator for modeling biofilm evolution in porous media including hydrodynamics and nutrient transport based on coupling of advection transport with Fickian diffusion and a reaction term to account for nutrient consumption. Biofilm has non‐zero permeability permitting liquid flow and transport through the biofilm itself. To handle simultaneous mass transfer in both liquid and biofilm in a pore element, a dual‐diffusion mass transfer model is introduced. The influence of nutrient limitation on predicted results is explored. Nutrient concentration in the network is affected by diffusion coefficient for nutrient transfer across biofilm (compared to water/water diffusion coefficient) under advection dominated transport, represented by mass transport Péclet number >1. The model correctly predicts a dependence of rate of biomass accumulation on inlet concentration. Poor network connectivity shows a significantly large reduction of permeability, for a small biomass pore volume. Biotechnol. Bioeng. 2011;108: 2413–2423. © 2011 Wiley Periodicals, Inc.     

Novel chromosomal translocation (17;22)(q12;q12) in a case of myelodisplastic syndrome characterized with signs of hemolytic anemia at presentation

Myelodysplastic syndromes (MDS) are clonal stem cell diseases that can result in cytopenias, dysplasia in one or more cell lineages, infective hematopoiesis, and increase the risk of progression to acute myeloid leukemia (AML). MDSs are characterized by several recurrent cytogenetic defects, which can affect diagnosis, prognosis, and treatment. Some of that chromosomal alterations are associated with very poor prognosis. Conventional cytogenetics cannot accurately define the rearranged karyotype. Instead, molecular cytogenetics analyses can provide important diagnostic and prognostic information for patients affected by MDS, allowing the characterization of the whole mutational spectrum and, mainly, novel chromosomal lesions.In this paper, we report a MDS case with a novel chromosomal translocation [t(17;22)(q12;q22)], described for the first time here. Following Giemsa-banding karyotyping, fluorescent in situ hybridization analyses, by using chromosome-specific probes, displayed the breakpoint regions at chromosomes 17 and 22, within which intra and inter-chromosomal segmental duplications (SD) are present. Because of the occurrence of SDs in breakpoint region, it was not possible to finely define the genomic regions where breaks fell. Further investigations could be required to better understand the molecular basis of the novel translocation t(17;22)(q12;q12) acting in MDS context and to explain if SDs could contribute to the pathogenesis of MDS.     

Identification and removal of nitroxide spin label contaminant: impact on PRE studies of α-helical membrane proteins in detergent

NMR paramagnetic relaxation enhancement (PRE) provides long‐range distance constraints (～15–25 Å) that can be critical to determining overall protein topology, especially where long‐range NOE information is unavailable such as in the case of larger proteins that require deuteration. However, several challenges currently limit the use of NMR PRE for α‐helical membrane proteins. One challenge is the nonspecific association of the nitroxide spin label to the protein‐detergent complex that can result in spurious PRE derived distance restraints. The effect of the nitroxide spin label contaminant is evaluated and quantified and a robust method for the removal of the contaminant is provided to advance the application of PRE restraints to membrane protein NMR structure determination.     

双管同步换血治疗新生儿高胆红素血症的临床分析

目的:探讨外周动静脉双管同步换血术治疗新生儿高胆红素血症临床疗效。方法:回顾性分析了采用外周动静脉双管同步换血术治疗的32例高胆红素血症患儿,比较换血前后血清胆红素的变化。结果:32例患者换血前后总胆红素有明显变化,显著下降(P<0.01)。不过在治疗后出现术后感染2例,经对症处理后痊愈。结论:新生儿外周动静脉双管同步换血术治疗新生儿高胆红素血症简单、实用、安全,值得进一步推广应用。     

不同浓度硒酸钠对茶树的生长和生理指标的影响

该文以一年生扦插苗为材料,采用水培试验,研究不同浓度的硒酸钠(0、0.15、0.3、1.5、3、5、8 mg·L^-1)对茶苗的硒积累、植株生长、生理指标和根尖显微结构等参数的影响。结果表明:茶苗的根和新梢中的硒含量与营养液中的硒浓度正相关;随着硒浓度升高,茶苗的鲜重、侧根数量、根系生物量、光合色素含量、根系活力等生长指标,茶多酚、可溶性蛋白、可溶性糖等茶叶质量指标均呈现先升后降趋势;而丙二醛、过氧化氢、脯氨酸含量等抗逆生理指标则呈现先降后升趋势。显微结构分析显示在不同硒浓度处理条件下根尖的显微构造存在差异。低硒浓度(0.15、0.3、1.5 mg·L^-1)处理的茶苗根尖的皮层薄壁细胞饱满、完好,表皮细胞较小;高硒浓度(Se≥3 mg·L^-1)处理的茶苗根尖的皮层薄壁细胞变形或受损,表皮细胞增厚,表现出胁迫反应。上述结果说明硒对茶树具有双重效应,合适浓度(0.3 mg·L^-1)硒对茶树生长和茶叶品质有益,表现为光合作用和根系活力增强,过氧化物和脯氨酸含量降低,生物量增加,茶叶茶多酚含量增加;硒浓度过高(≥3 mg·L^-1)对茶苗的生长和茶叶品质有害,表现为茶苗出现胁迫反应,茶多酚降低。该研究结果为进一步研究硒对茶树的双重作用机制和富硒茶的栽培提供参考。     

Characterization and comparison of putative Stenotrophomonas maltophilia methyl parathion hydrolases

Three Stenotrophomonas maltophilia isolates, KKWT11, CBF10-1, TTF10, were collected from organophosphate (OP)-contaminated soil in the Houston metropolitan area. A conserved metallo-β-lactamase (MBL) enzyme purported to function as a methyl parathion hydrolase was identified and found to be distantly homologous to the characterized Pseudomonas sp. WBC-3 methyl parathion hydrolase and shared no significant homology with other organophosphate hydrolases. Following expression of MBL enzymes cloned from S. maltophilia strains KKWT11, CBF10-1, and TTF10, respectively, an enzymatic preference for paraoxon was observed, with concentrations of 70, 40, and 30 µM of p-nitrophenol (PNP) formed after 48 h. Comparatively limited hydrolysis against the phosphorothioate methyl parathion was recorded with concentrations of PNP ranging from 9.5 to 3.5 µM after 48 h. A coexpressive construct harboring a modified organophosphorus hydrolase enzyme and the CBF10-1 MBL enzyme yielded only a slight improvement in degradation of methyl parathion, resulting in 75 µM of PNP formed compared with 69 µM formed by the organophosphorus hydrolase (OPH) control over 48 h. These results suggest that S. maltophilia MBL enzymes are currently insufficient for broad-spectrum hydrolysis of phosphorothioate insecticides. Future studies will thus seek to elucidate their catalytic efficiency against other notable phosphotriester oxons, including chlorpyrifos oxon, and malaoxon.     

Rapid proliferation and nucleolar organizer targeting centromeric retrotransposons in cotton

Centromeric chromatin in most eukaryotes is composed of highly repetitive centromeric retrotransposons and satellite repeats that are highly variable even among closely related species. The evolutionary mechanisms that underlie the rapid evolution of centromeric repeats remain unknown. To obtain insight into the evolution of centromeric repeats following polyploidy, we studied a model diploid progenitor (Gossypium raimondii, D‐genome) of the allopolyploid (AD‐genome) cottons, G. hirsutum and G. barbadense. Sequence analysis of chromatin‐immunoprecipitated DNA showed that the G. raimondii centromeric repeats originated from retrotransposon‐related sequences. Comparative analysis showed that nine of the 10 analyzed centromeric repeats were absent from the centromeres in the A‐genome and related diploid species (B‐, F‐ and G‐genomes), indicating that they colonized the centromeres of D‐genome lineage after the divergence of the A‐ and D‐ ancestral species or that they were ancestrally retained prior to the origin of Gossypium. Notably, six of the nine repeats were present in both the A‐ and D‐subgenomes in tetraploid G. hirsutum, and increased in abundance in both subgenomes. This finding suggests that centromeric repeats may spread and proliferate between genomes subsequent to polyploidization. Two repeats, Gr334 and Gr359 occurred in both the centromeres and nucleolar organizer regions (NORs) in D‐ and AD‐genome species, yet localized to just the NORs in A‐, B‐, F‐, and G‐genome species. Contained within is a story of an established centromeric repeat that is eliminated and allopolyploidization provides an opportunity for reinvasion and reestablishment, which broadens our evolutionary understanding behind the cycles of centromeric repeat establishment and targeting.     

A photo-cleavable biotin affinity tag for the facile release of a photo-crosslinked carbohydrate-binding protein

The use of photo-crosslinking glycoprobes represents a powerful strategy for the covalent capture of labile protein complexes and allows detailed characterization of carbohydrate-mediated interactions. The selective release of target proteins from solid support is a key step in functional proteomics. We envisaged that light activation can be exploited for releasing labeled protein in a dual photo-affinity probe-based strategy. To investigate this possibility, we designed a trifunctional, galactose-based, multivalent glycoprobe for affinity labeling of carbohydrate-binding proteins. The resulting covalent protein–probe adduct is attached to a photo-cleavable biotin affinity tag; the biotin moiety enables specific presentation of the conjugate on streptavidin-coated beads, and the photolabile linker allows the release of the labeled proteins. This dual probe promotes both the labeling and the facile cleavage of the target protein complexes from the solid surfaces and the remainder of the cell lysate in a completely unaltered form, thus eliminating many of the common pitfalls associated with traditional affinity-based purification methods.