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Purification of functional reprogramming factors in mammalian cell using FLAG -Tag
Han, M.J.,Kim, H.R.,O'Reilly, C.,Kim, C.H. Academic Press 2017 Biochemical and biophysical research communication Vol. No.
Induced pluripotent stem cells (iPSCs) technology is a method for generating pluripotent stem cells in vitro from fully differentiated cells such as fibroblast cells. The potential applications of iPSC technology in cell therapy and disease modeling could influence current medical practices. Despite current advances in iPSC technology, many patient-derived reprogrammed cells are not suitable for clinical trial because most protocols rely on virus-based techniques, which pose the risk of integration of the viral genome into the chromosomes. Therefore, non-viral methods such as mRNA and protein-based reprogramming are promising alternatives when generating clinically safe iPSCs. In a previous study, we generated human iPSCs using cell extracts with cell penetration peptide (CPP) for the delivery of reprogramming proteins [Kim et al. Cell Stem Cells, 2009]. In here, we show that the expression of reprogramming factors in mammalian cells and subsequent purification of these factors by FLAG-Tag could reprogram fibroblasts into iPSCs.
Marrs, Rob H.,O'Reilly, John,Rose, Rob J.,Lee, HyoHyeMi,Alday, Josu G. National Institute of Ecology 2022 국립생태원회보(PNIE) Vol.3 No.3
Saxifraga hirculus is classified as a vulnerable plant species in Europe, and it is confined to base-rich flushes in the British uplands. However, a lack of available information about its conservation status hampers the development of adaptive strategies for its in-situ conservation, especially with respect to grazing. To assess the effectiveness of sheep grazing in maintaining viable populations of S. hirculus, we compared the community dynamics of the vegetation in a base-rich flush over 44 years in two plots: one sheep-grazed under business-as-usual sheep grazing densities and the other fenced to exclude grazing. The plots were established in 1972, and the abundances of all vascular plants, bryophytes, and litter were measured at six intervals until 2016. Our results showed that although the presence of S. hirculus was maintained in both plots over the 44 years, it declined and reached a minimum between 1995 and 2010, when it was close to extinction. Since 2013, Saxifraga has recovered only slightly. Interestingly, the S. hirculus response appeared to be independent of grazing treatment, but it mirrored wider changes in the vegetation composition and structure within the flush over the 44 years. These changes are similar to others reported in broader uplands that have been attributed to a combination of reduced nitrogen and sulfur deposition and global warming. Thus, the simple adaptive management approach of "just managing" sheep grazing appeared ineffectual for preserving the S. hirculus population. S. hirculus showed signs of recovery at the end of the study period within this base-rich flush.
Marrs, Rob H.,McAllister, H.A.,Cho, K.,Rose, Rob J.,O'Reilly, J.,Furnes, M.,Lee, Hyohyemi National Institute of Ecology 2020 국립생태원회보(PNIE) Vol.1 No.1
Many areas of vegetation in the British uplands have reduced species diversity as a result of sheep overgrazing. It has been suggested that abandonment or re-wilding strategies might be used to reverse this. A likely first step would be the removal or reduction of grazing livestock from upland areas, with a presumption that this would lead to a recovery in species richness. However, we do not know if this would work, or the timescales involved. One of the important areas where more knowledge is needed is information on the size and composition of soil seedbanks as regeneration from zseed is a likely pathway of recovery. Here, we compared seedbanks in both grazed and ungrazed plots in five experiments at Moor House NNR in the northern Pennines; these sheep grazing exclusion experiments were started 52 and 63/64 years ago. Soil samples (n=10) were collected from both grazed and ungrazed plots in each experiment, and seed emergence counted in glasshouse trials. We detected only seeds of common species and very few dicotyledonous species. This suggests that the soil seedbank is unlikely to be a reliable source of the less common species for ecological restoration in these upland communities, suggesting an extinction debt. Therefore, seed addition and the creation of suitable safe-sites for germination may be needed in conjunction with grazing controls to allow the establishment of plants that will increase the species richness of the vegetation. However, this interventionist restoration approach remains to be tested.
The GENICA Network,kConFab Investigators,Norwegian Breast Cancer Study,Glubb, Dylan M.,Maranian, Mel J.,Michailidou, K.,Pooley, Karen A.,Meyer, Kerstin B.,Kar, S.,Carlebur, S.,O'Reilly, M.,Betts, Josh University of Chicago Press [etc.] 2015 American journal of human genetics Vol.96 No.1
Genome-wide association studies (GWASs) have revealed SNP rs889312 on 5q11.2 to be associated with breast cancer risk in women of European ancestry. In an attempt to identify the biologically relevant variants, we analyzed 909 genetic variants across 5q11.2 in 103,991 breast cancer individuals and control individuals from 52 studies in the Breast Cancer Association Consortium. Multiple logistic regression analyses identified three independent risk signals: the strongest associations were with 15 correlated variants (iCHAV1), where the minor allele of the best candidate, rs62355902, associated with significantly increased risks of both estrogen-receptor-positive (ER<SUP>+</SUP>: odds ratio [OR] = 1.24, 95% confidence interval [CI] = 1.21-1.27, p<SUB>trend</SUB> = 5.7 x 10<SUP>-44</SUP>) and estrogen-receptor-negative (ER<SUP>-</SUP>: OR = 1.10, 95% CI = 1.05-1.15, p<SUB>trend</SUB> = 3.0 x 10<SUP>-4</SUP>) tumors. After adjustment for rs62355902, we found evidence of association of a further 173 variants (iCHAV2) containing three subsets with a range of effects (the strongest was rs113317823 [p<SUB>cond</SUB> = 1.61 x 10<SUP>-5</SUP>]) and five variants composing iCHAV3 (lead rs11949391; ER<SUP>+</SUP>: OR = 0.90, 95% CI = 0.87-0.93, p<SUB>cond</SUB> = 1.4 x 10<SUP>-4</SUP>). Twenty-six percent of the prioritized candidate variants coincided with four putative regulatory elements that interact with the MAP3K1 promoter through chromatin looping and affect MAP3K1 promoter activity. Functional analysis indicated that the cancer risk alleles of four candidates (rs74345699 and rs62355900 [iCHAV1], rs16886397 [iCHAV2a], and rs17432750 [iCHAV3]) increased MAP3K1 transcriptional activity. Chromatin immunoprecipitation analysis revealed diminished GATA3 binding to the minor (cancer-protective) allele of rs17432750, indicating a mechanism for its action. We propose that the cancer risk alleles act to increase MAP3K1 expression in vivo and might promote breast cancer cell survival.