Fast Track to Discover Novel Promoters in Rice.
Ontology highlight
ABSTRACT:
SUBMITTER: Yoo YH
PROVIDER: S-EPMC7020180 | biostudies-literature | 2020 Jan
REPOSITORIES: biostudies-literature
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Project description:The 3 day workshop "Alzheimer's Fast Track" is a unique opportunity for graduate students, postdoctoral fellows, or other early-career scientists, focused on Alzheimer's disease research, to gain new knowledge and become an expert in where this emerging scientific field is moving. In addition, it is not only about receiving a good overview, but also learning to write and defend a successful application for securing funding for Alzheimer's disease research projects.
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Project description:Considerable technological advancements have recently been made with endovascular stent grafts for the treatment of abdominal aortic aneurysm (AAA). However, there is opportunity to further improve the efficiency of endovascular aneurysm repair (EVAR), which may yield better patient outcomes and lower perioperative treatment costs.The Least Invasive Fast-Track EVAR (LIFE) registry was developed to determine the clinical utility and cost effectiveness of the Ovation® Prime stent graft when used under least invasive conditions using a defined fast-track protocol. The LIFE study is a prospective multicenter post-market registry of the ultra-low profile (14F) Ovation Prime stent graft when used in the treatment of patients with AAA using a fast-track protocol, consisting of appropriate patient selection, bilateral percutaneous access, avoidance of general anesthesia and intensive care unit admission, and next-day discharge. The primary endpoint of the study is the proportion of subjects that experience a major adverse event within 30 days of the initial procedure. Primary endpoint data will be compared to a target performance goal. A total of 250 subjects will be enrolled at up to 40 sites in the United States. The first subject in this study was enrolled in October 2014 and enrollment is anticipated to continue through mid-2016.The recent development of ultra low-profile stent grafts enables EVAR using least invasive methods. A structured fast-track EVAR protocol may yield clinical and cost benefits versus standard EVAR.ClinicalTrials.gov Identifier: NCT02224794.
| S-EPMC4684921 | biostudies-literature
Project description:Novel constitutive gene promoters are essential components of crop biotechnology. Our analysis of five such promoters, APX, SCP1, PGD1, R1G1B, and EIF5, in transgenic rice plants is reported here. The five promoter regions were linked to the gfp reporter gene and transformed into rice. Using fluorescent microscopy and q-RT-PCR, promoter activities were analysed in comparison with OsCc1, Act1, and ZmUbi1, previously characterized as strong constitutive promoters. The APX and PGD1 promoters direct high levels of gene expression in all tissues and stages, producing GFP at levels of up to 1.3% of the total soluble protein. PGD1 is particularly active in flowers and mature roots. The R1G1B is active in the whole grain including the embryo, endosperm, and aleurone layer, and thus represents a constitutive promoter with activity in whole seeds that has not been described previously. The ZmUbi1 and R1G1B promoters are markedly less active in young roots and mature leaves whilst the APX, PGD1, OsCc1, and Act1 promoters are highly active in both vegetative and reproductive tissues. Overall, our results demonstrate that APX, PGD1, and R1G1B are novel gene promoters that are highly active at all stages of plant growth with distinct levels of activity.
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Project description:As an important part of synthetic biology, synthetic promoter has gradually become a hotspot in current biology. The purposes of the present study were to synthesize green tissue-specific promoters and to discover green tissue-specific cis-elements. We first assembled several regulatory sequences related to tissue-specific expression in different combinations, aiming to obtain novel green tissue-specific synthetic promoters. GUS assays of the transgenic plants indicated 5 synthetic promoters showed green tissue-specific expression patterns and different expression efficiencies in various tissues. Subsequently, we scanned and counted the cis-elements in different tissue-specific promoters based on the plant cis-elements database PLACE and the rice cDNA microarray database CREP for green tissue-specific cis-element discovery, resulting in 10 potential cis-elements. The flanking sequence of one potential core element (GEAT) was predicted by bioinformatics. Then, the combination of GEAT and its flanking sequence was functionally identified with synthetic promoter. GUS assays of the transgenic plants proved its green tissue-specificity. Furthermore, the function of GEAT flanking sequence was analyzed in detail with site-directed mutagenesis. Our study provides an example for the synthesis of rice tissue-specific promoters and develops a feasible method for screening and functional identification of tissue-specific cis-elements with their flanking sequences at the genome-wide level in rice.
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Project description:Many embryonic species are initially transcriptionally quiescent after fertilization. In this issue of Developmental Cell, Blythe et al. reveal that beta-catenin acts very early in Xenopus development to specifically modify the chromatin of organizer genes, poising them for rapid activation when transcription begins.
| S-EPMC5568668 | biostudies-other
Project description:Postoperative joint stiffness following total knee arthroplasty (TKA) may compromise the outcome and necessitate manipulation. Previous studies have not been in a fast-track setting with optimized pain treatment, early mobilization, and short length of stay (LOS), which may have influenced the prevalence of joint stiffness and subsequent manipulation. We investigated the prevalence of manipulation following fast-track TKA and identified patients at risk of needing manipulation.3,145 consecutive unselected elective primary unilateral TKA patients operated in 6 departments with well-defined fast-track settings were included in the study. Demographic data, prevalence, type and timing of manipulation, and preoperative and postoperative ROM were recorded prospectively, ensuring complete 1-year follow-up.70 manipulations were performed within 1 year (2.2%) at a mean of 4 months after index surgery. Younger age and not using walking aids preoperatively were associated with a higher risk of manipulation. LOS ? 4 days (as opposed to a longer LOS) was not associated with an increased risk of manipulation.The prevalence of manipulation was lower or comparable to that in most published studies following more conventional pathways. Inherent patient demographics were identified as risk factors for manipulation whereas LOS ? 4 days was not. Thus, fast-track TKA does not result in increased risk of manipulation-despite a shorter LOS. Optimized pain treatment and early mobilization may contribute to these favorable results that support the use of fast-track.
| S-EPMC4366662 | biostudies-literature
Project description:BackgroundRepositioning of existing drugs has been suggested as a fast track for developing new anti-malarial agents. The compound libraries of GlaxoSmithKline (GSK), Pfizer and AstraZeneca (AZ) comprising drugs that have undergone clinical studies in other therapeutic areas, but not achieved approval, and a set of US Food and Drug Administration (FDA)-approved drugs and other bio-actives were tested against Plasmodium falciparum blood stages.MethodsMolecules were tested initially against erythrocytic co-cultures of P. falciparum to measure proliferation inhibition using one of the following methods: SYBR®I dye DNA staining assay (3D7, K1 or NF54 strains); [(3)H] hypoxanthine radioisotope incorporation assay (3D7 and 3D7A strain); or 4',6-diamidino-2-phenylindole (DAPI) DNA imaging assay (3D7 and Dd2 strains). After review of the available clinical pharmacokinetic and safety data, selected compounds with low ?M activity and a suitable clinical profile were tested in vivo either in a Plasmodium berghei four-day test or in the P. falciparum Pf3D7(0087/N9) huSCID 'humanized' mouse model.ResultsOf the compounds included in the GSK and Pfizer sets, 3.8% (9/238) had relevant in vitro anti-malarial activity while 6/100 compounds from the AZ candidate drug library were active. In comparison, around 0.6% (24/3,800) of the FDA-approved drugs and other bio-actives were active. After evaluation of available clinical data, four investigational drugs, active in vitro were tested in the P. falciparum humanized mouse model: UK-112,214 (PAF-H1 inhibitor), CEP-701 (protein kinase inhibitor), CEP-1347 (protein kinase inhibitor), and PSC-833 (p-glycoprotein inhibitor). Only UK-112,214 showed significant efficacy against P. falciparum in vivo, although at high doses (ED90 131.3 mg/kg [95% CI 112.3, 156.7]), and parasitaemia was still present 96 hours after treatment commencement. Of the six actives from the AZ library, two compounds (AZ-1 and AZ-3) were marginally efficacious in vivo in a P. berghei model.ConclusionsRepositioning of existing therapeutics in malaria is an attractive proposal. Compounds active in vitro at ?M concentrations were identified. However, therapeutic concentrations may not be effectively achieved in mice or humans because of poor bio-availability and/or safety concerns. Stringent safety requirements for anti-malarial drugs, given their widespread use in children, make this a challenging area in which to reposition therapy.
| S-EPMC4021201 | biostudies-literature
Project description:Background In pediatric cardiac surgery, perioperative management has evolved from slow weaning of mechanical ventilation in the intensive care unit to "ultra-fast-track" anesthesia with early extubation (EE) in theater to promote a faster recovery. The strategy of EE has not been assessed in adults with congenital heart disease, a growing population of patients who often require surgery. Methods And Results Data were collected retrospectively on all patients >16 years of age who underwent adult congenital heart surgery in our tertiary center between December 2012 and January 2020. Coarsened exact matching was performed for relevant baseline variables. Overall, 711 procedures were performed: 133 (18.7%) patients underwent EE and 578 (81.3%) patients received conventional extubation. After matching, patients who received EE required less inotropic or vasopressor support in the early postoperative period (median Vasoactive-inotropic score 0.5 [0.0-2.0] versus 2.0 [0.0-3.5]; P<0.0001) and had a lower total net fluid balance than patients after conventional extubation (1168±723 versus 847±733 mL; P=0.0002). The overall reintubation rate was low at 0.3%. EE was associated with a significantly shorter postoperative length of stay in higher dependency care units before a "step-down" to ward-based care (48 [45-50] versus 50 [47-69] hours; P=0.004). Lower combined intensive care unit and high dependency unit costs were incurred by patients who received EE compared with patients who received conventional extubation (£3949 [3430-4222] versus £4166 [3893-5603]; P<0.0001). Conclusions In adult patients undergoing surgery for congenital heart disease, EE is associated with a reduced need for postoperative hemodynamic support, a shorter intensive care unit stay, and lower health-care-related costs.
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Project description:Given the scale and rapid spread of the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, or 2019-nCoV), there is an urgent need to identify therapeutics that are effective against COVID-19 before vaccines are available. Since the current rate of SARS-CoV-2 knowledge acquisition via traditional research methods is not sufficient to match the rapid spread of the virus, novel strategies of drug discovery for SARS-CoV-2 infection are required. Structure-based virtual screening for example relies primarily on docking scores and does not take the importance of key residues into consideration, which may lead to a significantly higher incidence rate of false-positive results. Our novel in silico approach, which overcomes these limitations, can be utilized to quickly evaluate FDA-approved drugs for repurposing and combination, as well as designing new chemical agents with therapeutic potential for COVID-19. As a result, anti-HIV or antiviral drugs (lopinavir, tenofovir disoproxil, fosamprenavir and ganciclovir), antiflu drugs (peramivir and zanamivir) and an anti-HCV drug (sofosbuvir) are predicted to bind to 3CLPro in SARS-CoV-2 with therapeutic potential for COVID-19 infection by our new protocol. In addition, we also propose three antidiabetic drugs (acarbose, glyburide and tolazamide) for the potential treatment of COVID-19. Finally, we apply our new virus chemogenomics knowledgebase platform with the integrated machine-learning computing algorithms to identify the potential drug combinations (e.g. remdesivir+chloroquine), which are congruent with ongoing clinical trials. In addition, another 10 compounds from CAS COVID-19 antiviral candidate compounds dataset are also suggested by Molecular Complex Characterizing System with potential treatment for COVID-19. Our work provides a novel strategy for the repurposing and combinations of drugs in the market and for prediction of chemical candidates with anti-COVID-19 potential.
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Project description:Despite much interest in regulatory evolution, how promoters have evolved remains poorly studied, mainly owing to paucity of data on promoter regions. Using a new set of high-quality experimentally determined core promoters of the human genome, we conducted a comparative analysis of 2,492 human and rhesus macaque promoters and their neighboring nearly neutral regions. We found that the core promoters have an average rate of nucleotide substitution substantially higher than that at 4-fold degenerate sites and only slightly lower than that for the assumed neutral controls of neighboring noncoding regions, suggesting that core promoters are subject to very weak selective constraints. Interestingly, we identified 24 core promoters (at false discovery rate = 50%) that have evolved at an accelerated rate compared with the neutral controls, suggesting that they may have undergone positive selection. The inferred positively selected genes show strong bias in molecular function. We also used population genetic approaches to examine the evolution of core promoters in human populations and found evidence of positive selection at some loci. Taken together, our results suggest that positive selection has played a substantial role in the evolution of transcriptional regulation in primates.
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