Conservative site-specific and single-copy transgenesis in human LINE-1 elements

Genome engineering of human cells plays an important role in biotechnology and molecular medicine. In particular, insertions of functional multi-transgene cassettes into suitable endogenous sequences will lead to novel applications. Although several tools have been exploited in this context, safety issues such as cytotoxicity, insertional mutagenesis and off-target cleavage together with limitations in cargo size/expression often compromise utility. Phage λ integrase (Int) is a transgenesis tool that mediates conservative site-specific integration of 48 kb DNA into a safe harbor site of the bacterial genome. Here, we show that an Int variant precisely recombines large episomes into a sequence, termed attH4X, found in 1000 human Long INterspersed Elements-1 (LINE-1). We demonstrate single-copy transgenesis through attH4X-targeting in various cell lines including hESCs, with the flexibility of selecting clones according to transgene performance and downstream applications. This is exemplified with pluripotency reporter cassettes and constitutively expressed payloads that remain functional in LINE1-targeted hESCs and differentiated progenies. Furthermore, LINE-1 targeting does not induce DNA damage-response or chromosomal aberrations, and neither global nor localized endogenous gene expression is substantially affected. Hence, this simple transgene addition tool should become particularly useful for applications that require engineering of the human genome with multi-transgenes.     

Soil ciliates of the Indian Delhi Region: Their community characteristics with emphasis on their ecological implications as sensitive bio-indicators for soil quality

The present investigation aims to study the diversity of ciliates from different habitats in and around Delhi, India, and the correlation of this diversity with soil quality {agricultural lands (site 1 and 2), dump yards (site 3 and 4), sewage treatment plant (site 5), residential land (site 6), landfill (site 7) and barren land (site 8)}. Various physicochemical parameters of the different soil samples were studied and analysed for soil texture, interstitial water, pH, conductivity, total organic carbon, total organic matter, total nitrogen and phosphorous content, using standard protocols. Seventeen ciliate taxa belonging to four classes, seven orders, ten families, and 17 genera were recorded, with the maximum number of species (eleven) belonging to the class Spirotrichea. Ciliate diversity was highest at sites 5 and 6 and lowest at sites 1 and 2. Spathidium sp. was the dominant species in the conditioned land (site 8), while the ciliate Colpoda sp. was present in all the sites examined, showing the highest population density in the sewage treatment plant site (site 5). Statistical analysis showed that ciliate diversity was positively correlated to physicochemical parameters such as interstitial water, total organic matter and organic carbon, total nitrogen and total phosphorous content. Analyses of spirotrichs/colpodids (S/C) ratio and diversity indices implied that the habitat conditions of sites 1, 2, 3 and 8 are relatively unfavourable for soil ciliates to flourish; while sites 4, 5, 6 and 7 provided more favourable conditions. The ubiquity of ciliate distribution suggests their important role in the soil food webs and nutrient cycling, and their community structure and specific characteristics appear to be of major importance for soil formation. A full understanding of soil ciliate diversity and physicochemical parameters helps to inform best practice for improving soil quality as well as conservation practices for sustainable development and management of farms and cultivated lands. In conclusion, ciliate diversity serves as an important and sensitive bio-indicator for soil quality.     

Insulin Regulates Nitric Oxide Production in the Kidney Collecting Duct Cells

The kidney is an important organ for arterial blood pressure (BP) maintenance. Reduced NO generation in the kidney is associated with hypertension in insulin resistance. NO is a critical regulator of vascular tone; however, whether insulin regulates NO production in the renal inner medullary collecting duct (IMCD), the segment with the greatest enzymatic activity for NO production in kidney, is not clear. Using an NO-sensitive 4-amino-5-methylamino-2′,7′-difluorofluorescein (DAF-FM) fluorescent dye, we found that insulin increased NO production in mouse IMCD cells (mIMCD) in a time- and dose-dependent manner. A concomitant dose-dependent increase in the NO metabolite (NOx) was also observed in the medium from insulin-stimulated cells. NO production peaked in mIMCD cells at a dose of 100 nm insulin with simultaneously increased NOx levels in the medium. At this dose, insulin significantly increased p-eNOS^Ser1177 levels in mIMCD cells. Pretreatment of cells with a PI 3-kinase inhibitor or insulin receptor silencing with RNA interference abolished these effects of insulin, whereas insulin-like growth factor-1 receptor (IGF-1R) silencing had no effect. We also showed that chronic insulin infusion to normal C57BL/6J mice resulted in increased endothelial NOS (eNOS) protein levels and NO production in the inner medulla. However, insulin-infused IRKO mice, with targeted deletion of insulin receptor from tubule epithelial cells of the kidney, had ∼50% reduced eNOS protein levels in their inner medulla along with a significant rise in BP relative to WT littermates. We have previously reported increased baseline BP and reduced urine NOx in IRKO mice. Thus, reduced insulin receptor signaling in IMCD could contribute to hypertension in the insulin-resistant state.     

Effects of Litter Addition on Ectomycorrhizal Associates of a Lodgepole Pine (Pinus contorta) Stand in Yellowstone National Park

Increasing soil nutrients through litter manipulation, pollution, or fertilization can adversely affect ectomycorrhizal (EM) communities by inhibiting fungal growth. In this study, we used molecular genetic methods to determine the effects of litter addition on the EM community of a Pinus contorta stand in Yellowstone National Park that regenerated after a stand-replacing fire. Two controls were used; in unmodified control plots nothing was added to the soil, and in perlite plots perlite, a chemically neutral substance, was added to maintain soil moisture and temperature at levels similar to those under litter. We found that (i) species richness did not change significantly following perlite addition (2.6 ± 0.3 species/core in control plots, compared with 2.3 ± 0.3 species/core in perlite plots) but decreased significantly (P < 0.05) following litter addition (1.8 ± 0.3 species/core); (ii) EM infection was not affected by the addition of perlite but increased significantly (P < 0.001) in response to litter addition, and the increase occurred only in the upper soil layer, directly adjacent to the added litter; and (iii) Suillus granulatus, Wilcoxina mikolae, and agaricoid DD were the dominant organisms in controls, but the levels of W. mikolae and agaricoid DD decreased significantly in response to both perlite and litter addition. The relative levels of S. granulatus and a fourth fungus, Cortinariaceae species 2, increased significantly (P < 0.01 and P < 0.05, respectively) following litter addition. Thus, litter addition resulted in some negative effects that may be attributable to moisture-temperature relationships rather than to the increased nutrients associated with litter. Some species respond positively to litter addition, indicating that there are differences in their physiologies. Hence, changes in the EM community induced by litter accumulation also may affect ecosystem function.     

Antioxidant and antibacterial properties of some cultured lichens

The lichen species namely Usnea ghattensis, Heterodermia podocarpa, Arthothelium awasthii and Parmotrema tinctorum have been cultured in vitro and were screened for their antioxidant and antibacterial potential using different assay systems. The methanol extract of lichens showed antioxidant and antibacterial activities according to the order U. ghattensis>A. awasthii>H. podocarpa>P. tinctorum. The IC(50) values for the antioxidant activities of U. ghattensis and A. awasthii are less or equivalent to that of standard antioxidants. The methanolic extracts of the mycobiont and photobiont cultures of lichenU. ghattensis and A. awasthii were effective against Bacillus licheniformis, Bacillus megaterium, Bacillus subtilis and Staphylococcus aureus. The minimum inhibitory concentration (MIC) of the extract was found between 5 and 10microg extract/ml. The results suggested that the extract of mycobiont and photobiont cultures of lichen U. ghattensis and A. awasthii could be of use as an easily accessible source of natural antioxidants and antibacterial properties for the possible food supplement or in the pharmaceutical industry.     

Antioxidant and antibacterial activities of lichen <Emphasis Type="Italic">Usnea ghattensis</Emphasis><Emphasis Type="Italic">in vitro</Emphasis>

Various solvent extracts of the lichen Usnea ghattensis showed good antioxidant activity. A methanol extract prevented lipid peroxidation by 87% followed by 65% in Trolox at 20 μg/ml. It also showed superoxide anion scavenging activity and free radical scavenging activity 56% and 73%, respectively. The known antioxidants butylated hydroxytoluene (BHT), butylated hydroxyanisol (BHA) and quercetin at similar concentrations showed superoxide anion scavenging activity of 68, 59 and 47% and free radical scavenging activity 83, 77 and 69%, respectively. In addition, these extracts were inhibitory against Bacillus licheniformis, Bacillus megaterium, Bacillus subtilis and Staphylococcus aureus with MIC values of 5–10 μg/ml.Received after revisions 10 May 2005     

Effects of litter addition on ectomycorrhizal associates of a lodgepole pine (Pinus contorta) stand in Yellowstone National Park

Increasing soil nutrients through litter manipulation, pollution, or fertilization can adversely affect ectomycorrhizal (EM) communities by inhibiting fungal growth. In this study, we used molecular genetic methods to determine the effects of litter addition on the EM community of a Pinus contorta stand in Yellowstone National Park that regenerated after a stand-replacing fire. Two controls were used; in unmodified control plots nothing was added to the soil, and in perlite plots perlite, a chemically neutral substance, was added to maintain soil moisture and temperature at levels similar to those under litter. We found that (i) species richness did not change significantly following perlite addition (2.6 +/- 0.3 species/core in control plots, compared with 2.3 +/- 0.3 species/core in perlite plots) but decreased significantly (P < 0.05) following litter addition (1.8 +/- 0.3 species/core); (ii) EM infection was not affected by the addition of perlite but increased significantly (P < 0.001) in response to litter addition, and the increase occurred only in the upper soil layer, directly adjacent to the added litter; and (iii) Suillus granulatus, Wilcoxina mikolae, and agaricoid DD were the dominant organisms in controls, but the levels of W. mikolae and agaricoid DD decreased significantly in response to both perlite and litter addition. The relative levels of S. granulatus and a fourth fungus, Cortinariaceae species 2, increased significantly (P < 0.01 and P < 0.05, respectively) following litter addition. Thus, litter addition resulted in some negative effects that may be attributable to moisture-temperature relationships rather than to the increased nutrients associated with litter. Some species respond positively to litter addition, indicating that there are differences in their physiologies. Hence, changes in the EM community induced by litter accumulation also may affect ecosystem function.     

Experimental studies on the growth and usnic acid production in "lichen"Usnea ghattensis in vitro

The study was aimed to optimize the culture conditions for the production of usnic acid in the cultured cell aggregates composed of symbionts in lichen Usnea ghattensis in vitro. The cultured lichen tissue composed of symbionts appeared after about 2-3 weeks of inoculation in water-agar and malt-yeast extract (MYE) media and shown the production of usnic acid after 2-3 months of inoculation. However, the growth of symbionts was strongly affected by different culture conditions. The addition of excess carbon and nitrogen sources in the media has significantly enhanced the growth as well as usnic acid content. The cultured symbionts in MYE medium having 4% sucrose, 4% polyethyl glycol (PEG) gave 7.63 g dry biomass with 3.9 microg usnic acid/g dry biomass. In water-agar medium having 4% sucrose and 4% PEG gave 3.08 g dry biomass with 1.11 microg usnic acid/g dry biomass. The positive effects of medium on the growth of symbionts and the production of usnic acid are seemed to be due to nutritional factors.