Synthesis and conformational evaluation of a novel gene delivery vector for human mesenchymal stem cells

We have synthesized a novel gene delivery vector by covalently combining branched polyethylenimine (bPEI) and hyaluronic acid (HA) with the aim of improving transfection of bPEI into human mesenchymal stem cells (hMSCs) while maintaining cell viability. Because of the opposite charges on bPEI and HA, the bPEI-HA vector forms a zwitterionic polymer capable of inter- and intramolecular interactions. We have characterized the hydrodynamic radius of bPEI-HA and bPEI-HA/DNA complexes at ambient and physiological temperatures, as well as at a range of salt concentrations using light scattering, and investigated the effect of the size of transfecting complexes on gene delivery. We found that by increasing the salt concentration from 150 to 1000 mM of NaCl, the mean hydrodynamic radius (R(h)) of bPEI-HA increases from 2.0 +/- 1.1 to 366.0 +/- 149.0 nm. However, increasing the salt concentration decreases the mean R(h) of bPEI-HA/DNA complexes from 595.0 +/- 44.6 to 106.0 +/- 19.2 nm at 25 degrees C and from 767.0 +/- 137.2 to 74.0 +/- 23.0 nm at 37 degrees C. hMSCs transfected with smaller complexes showed a significant increase in transfection from 3.8 +/- 1.5% to 19.1 +/- 4.4%. Similarly, bPEI-HA performed significantly better than bPEI in terms of cell viability (86.0 +/- 6.7% with bPEI-HA versus 7.0 +/- 2.8% with bPEI, 24 h post exposure at the highest concentration of 500 mg/mL) and maximum transfection efficiencies (12.0 +/- 4.2% with bPEI/DNA complexes and 33.6 +/- 13.9% with bPEI-HA/DNA complexes). Thus, modifying bPEI by covalent conjugation with HA improves its performance as a gene delivery vector in hMSCs. This presents a promising approach to altering hMSCs for tissue engineering and other applications.     

Synthesis and characterization of injectable, thermally and chemically gelable, amphiphilic poly(N-isopropylacrylamide)-based macromers

In this study, we synthesized and characterized a series of macromers based on poly( N-isopropylacrylamide) that undergo thermally induced physical gelation and, following chemical modification, can be chemically cross-linked. Macromers with number average molecular weights typically ranging from 2000-3500 Da were synthesized via free radical polymerization from, in addition to N-isopropylacrylamide, pentaerythritol diacrylate monostearate, a bifunctional monomer containing a long hydrophobic chain, acrylamide, a hydrophilic monomer, and hydroxyethyl acrylate, a hydrophilic monomer used to provide hydroxyl groups for further chemical modification. Results indicated that the hydrophobic-hydrophilic balance achieved by varying the relative concentrations of comonomers used during synthesis was an important parameter in controlling the transition temperature of the macromers in solution and stability of the resultant gels. Storage moduli of the macromers increased over 4 orders of magnitude once gelation occurred above the transition temperature. Furthermore, chemical cross-linking of these macromers resulted in gels with increased stability compared to uncross-linked controls. These results demonstrate the feasibility of synthesizing poly( N-isopropylacrylamide)-based macromers that undergo tandem gelation and establish key criteria relating to the transition temperature and stability of these materials. The data suggest that these materials may be attractive substrates for tissue engineering and cellular delivery applications as the combination of mechanistically independent gelation techniques used in tandem may offer superior materials with regard to gelation kinetics and stability.     

Pan-European regional-scale modelling of water and N efficiencies of rapeseed cultivation for biodiesel production

The energy produced from the investment in biofuel crops needs to account for the environmental impacts on soil, water, climate change and ecosystem services. A regionalized approach is needed to evaluate the environmental costs of large-scale biofuel production. We present a regional pan-European simulation of rapeseed ( Brassica napus ) cultivation. Rapeseed is the European Union's dominant biofuel crop with a share of about 80% of the feedstock. To improve the assessment of the environmental impact of this biodiesel production, we performed a pan-European simulation of rapeseed cultivation at a 10 × 10 km scale with Environmental Policy Integrated Climate (EPIC). The model runs with a daily time step and model input consists of spatialized meteorological measurements, and topographic, soil, land use, and farm management practices data and information. Default EPIC model parameters were calibrated based on literature. Modelled rapeseed yields were satisfactory compared with yields at regional level reported for 151 regions obtained for the period from 1995 to 2003 for 27 European Union member countries, along with consistent modelled and reported yield responses to precipitation, radiation and vapour pressure deficit at regional level. The model is currently set up so that plant nutrient stress is not occurring. Total fertilizer consumption at country level was compared with IFA/FAO data. This approach allows us to evaluate environmental pressures and efficiencies arising from and associated with rapeseed cultivation to further complete the environmental balance of biofuel production and consumption.     

Phylogenetic analyses suggest that Psammomitra (Ciliophora,Urostylida) should represent an urostylid family,based on small subunit rRNA and alpha‐tubulin gene sequence information

The morphologically unique ciliate Psammomitra has long been considered as a systematically uncertain stichotrich. This is mainly because of its highly specialized morphology and a lack of either detailed information concerning its ontogenesis, or molecular data. Based on the small subunit rRNA (SSrRNA) gene and alpha‐tubulin gene sequences, we re‐evaluated the phylogenetic position of Psammomitra retractilis using multiple algorithms. Phylogenetic trees inferred from the SSrRNA gene sequences representing a total of 53 spirotrichs demonstrated the closest relationship of Psammomitra was with Holosticha‐like taxa, with strong support, which clearly suggested that Psammomitra should be placed into the order Urostylida although it branched at a rather deep level, and is likely to be closely related to Holostichidae. With consideration to molecular evidence and morphological characters, Psammomitra should be a clearly outlined taxon at about the rank of family, i.e. Psammomitridae stat. nov. , within the order Urostylida. The improved diagnosis for this family is as follows: Urostylida possessing extremely contractile, elongated body which consists of three parts: head, trunk, and slender tail; midventral complex composed of midventral pairs only and restricted to about anterior 1/3 of ventral surface; frontal, frontoterminal, and transverse cirri present; one left and one right marginal rows which commence near proximal end of adoral zone and extend to near rear body end.     

Molecular characterization of a fungal gene paralogue of the penicillin penDE gene of Penicillium chrysogenum

Background  

Penicillium chrysogenum converts isopenicillin N (IPN) into hydrophobic penicillins by means of the peroxisomal IPN acyltransferase (IAT), which is encoded by the penDE gene. In silico analysis of the P. chrysogenum genome revealed the presence of a gene, Pc13g09140, initially described as paralogue of the IAT-encoding penDE gene. We have termed this gene ial because it encodes a protein with high similarity to IAT (IAL for IAT-Like). We have conducted an investigation to characterize the ial gene and to determine the role of the IAL protein in the penicillin biosynthetic pathway.     

Effect of hydrocarbon concentration of pasture production (<i>Brachiaria humidicola</i>) in Texistepec,Veracruz

In this study, the relationship between the concentration of extra-heavy crude petroleum in a clayey material and the toxicity, field capacity, temperature, and growth of a tropical forage grass (Brachiara humidicola) was determined empirically. For this type of petroleum the acute toxicity (Microtox^®) was slight (CE₅₀ = 63200 - 76400 mg/kg) even at high hydrocarbon concentrations (29279 mg/kg). Nonetheless, serious impacts were encountered in terms of an increase in soil temperature (+ 1.3 °C), reduction in field capacity (-10.7%) and reduction in aerial biomass (-97%). The relationship between hydrocarbon concentration and biomass resulted in a typical dose-response curve (r = 0.99), where a concentration of 2626 mg/kg of hydrocarbons corresponds to a maintenance of 90% biomass. Furthermore, during the duration of this study (one year) the biodegradation was proportional to the pasture biomass production (r = 0.997) indicating a synergistic relationship between the petroleum biodegrading microorganisms in the rhizosphere and the pasture.     

Generation of stable, high-producing CHO cell lines by lentiviral vector-mediated gene transfer in serum-free suspension culture

Lentivirus‐derived vectors (LVs) were studied for the generation of stable recombinant Chinese hamster ovary (CHO) cell lines. Stable pools and clones expressing the enhanced green fluorescent protein (eGFP) were selected via fluorescence‐activated cell sorting (FACS). For comparison, cell pools and cell lines were also generated by transfection, using the LV transfer plasmid alone. The level and stability of eGFP expression was greater in LV‐transduced cell lines and pools than in those established by transfection. CHO cells were also infected at two different multiplicities of infection with an LV co‐expressing eGFP and a tumor necrosis factor receptor:Fc fusion protein (TNFR:Fc). At 2‐day post‐infection, clonal cell lines with high eGFP‐specific fluorescence were recovered by FACS. These clones co‐expressed TNFR:Fc with yields of 50–250 mg/L in 4‐day cultures. The recovered cell lines maintained stable expression over 3 months in serum‐free suspension culture without selection. In conclusion, LV‐mediated gene transfer provided an efficient alternative to plasmid transfection for the generation of stable and high‐producing recombinant cell lines. Biotechnol. Bioeng. 2011; 108:600–610. © 2010 Wiley Periodicals, Inc.     

Genetic Improvement of Willow for Bioenergy and Biofuels

Willows (Salix spp.) are a very diverse group of catkin-bearing trees and shrubs that are widely distributed across temperate regions of the globe.Some species respond well to being grown in short rotation coppice (SRC) cycles,which are much shorter than conventional forestry.Coppicing reinvigorates growth and the biomass rapidly accumulated can be used as a source of renewable carbon for bioenergy and biofuels.As SRC willows re-distribute nutrients during the perennial cycle they require only minimal nitro...     

Methylation-capture and Next-Generation Sequencing of free circulating DNA from human plasma

Background

Free circulating DNA (fcDNA) has many potential clinical applications, due to the non-invasive way in which it is collected. However, because of the low concentration of fcDNA in blood, genome-wide analysis carries many technical challenges that must be overcome before fcDNA studies can reach their full potential. There are currently no definitive standards for fcDNA collection, processing and whole-genome sequencing. We report novel detailed methodology for the capture of high-quality methylated fcDNA, library preparation and downstream genome-wide Next-Generation Sequencing. We also describe the effects of sample storage, processing and scaling on fcDNA recovery and quality.

Results

Use of serum versus plasma, and storage of blood prior to separation resulted in genomic DNA contamination, likely due to leukocyte lysis. Methylated fcDNA fragments were isolated from 5 donors using a methyl-binding protein-based protocol and appear as a discrete band of ~180 bases. This discrete band allows minimal sample loss at the size restriction step in library preparation for Next-Generation Sequencing, allowing for high-quality sequencing from minimal amounts of fcDNA. Following sequencing, we obtained 37×10⁶-86×10⁶ unique mappable reads, representing more than 50% of total mappable reads. The methylation status of 9 genomic regions as determined by DNA capture and sequencing was independently validated by clonal bisulphite sequencing.

Conclusions

Our optimized methods provide high-quality methylated fcDNA suitable for whole-genome sequencing, and allow good library complexity and accurate sequencing, despite using less than half of the recommended minimum input DNA.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-476) contains supplementary material, which is available to authorized users.