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1.
Sandrine Reigadas Guerric Anies Bernard Masquelier Christina Calmels Lieven J. Stuyver Vincent Parissi Herve Fleury Marie-Line Andreola 《PloS one》2010,5(4)
Resistance to HIV-1 integrase (IN) inhibitor raltegravir (RAL), is encoded by mutations in the IN region of the pol gene. The emergence of the N155H mutation was replaced by a pattern including the Y143R/C/H mutations in three patients with anti-HIV treatment failure. Cloning analysis of the IN gene showed an independent selection of the mutations at loci 155 and 143. Characterization of the phenotypic evolution showed that the switch from N155H to Y143C/R was linked to an increase in resistance to RAL. Wild-type (WT) IN and IN with mutations Y143C or Y143R were assayed in vitro in 3′end-processing, strand transfer and concerted integration assays. Activities of mutants were moderately impaired for 3′end-processing and severely affected for strand transfer. Concerted integration assay demonstrated a decrease in mutant activities using an uncleaved substrate. With 3′end-processing assay, IC50 were 0.4 µM, 0.9 µM (FC = 2.25) and 1.2 µM (FC = 3) for WT, IN Y143C and IN Y143R, respectively. An FC of 2 was observed only for IN Y143R in the strand transfer assay. In concerted integration, integrases were less sensitive to RAL than in ST or 3′P but mutants were more resistant to RAL than WT. 相似文献
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Laid Douidah Lieven De Zutter Filip Van Nieuwerburgh Dieter Deforce Hanne Ingmer Olivier Vandenberg Anne-Marie Van den Abeele Kurt Houf 《PloS one》2014,9(1)
In this study, we report the screening of four Arcobacter species for the presence of small and large plasmids. Plasmids were present in 9.9% of the 273 examined strains. One Arcobacter cryaerophilus and four Arcobacter butzleri plasmids were selected for further sequencing. The size of three small plasmids isolated from A. butzleri and the one from A. cryaerophilus strains ranged between 4.8 and 5.1 kb, and the size of the large plasmid, isolated from A. butzleri, was 27.4 kbp. The G+C content of all plasmids ranged between 25.4% and 26.2%. A total of 95% of the large plasmid sequence represents coding information, which contrasts to the 20 to 30% for the small plasmids. Some of the open reading frames showed a high homology to putative conserved domains found in other related organisms, such as replication, mobilization and genes involved in type IV secretion system. The large plasmid carried 35 coding sequences, including seven genes in a contiguous region of 11.6 kbp that encodes an orthologous type IV secretion system found in the Wolinella succinogenes genome, Helicobacter pylori and Campylobacter jejuni plasmids, which makes this plasmid interesting for further exploration. 相似文献
3.
Microbial Methylotrophic Metabolism: Recent Metabolic Modeling Efforts and Their Applications In Industrial Biotechnology
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Developing methylotrophic bacteria into cell factories that meet the chemical demand of the future could be both economical and environmentally friendly. Methane is not only an abundant, low‐cost resource but also a potent greenhouse gas, the capture of which could help to reduce greenhouse gas emissions. Rational strain design workflows rely on the availability of carefully combined knowledge often in the form of genome‐scale metabolic models to construct high‐producer organisms. In this review, the authors present the most recent genome‐scale metabolic models in aerobic methylotrophy and their applications. Further, the authors present models for the study of anaerobic methanotrophy through reverse methanogenesis and suggest organisms that may be of interest for expanding one‐carbon industrial biotechnology. Metabolic models of methylotrophs are scarce, yet they are important first steps toward rational strain‐design in these organisms. 相似文献
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Context
Health care technological evolution through new drugs, implants and other interventions is a key driver of healthcare spending. Policy makers are currently challenged to strengthen the evidence for and cost-effectiveness of reimbursement decisions, while not reducing the capacity for real innovations. This article examines six cases of reimbursement decision making at the national health insurance authority in Belgium, with outcomes that were contested from an evidence-based perspective in scientific or public media.Methods
In depth interviews with key stakeholders based on the adapted framework of Davies allowed us to identify the relative impact of clinical and health economic evidence; experience, expertise & judgment; financial impact & resources; values, ideology & political beliefs; habit & tradition; lobbyists & pressure groups; pragmatics & contingencies; media attention; and adoption from other payers & countries.Findings
Evidence was not the sole criterion on which reimbursement decisions were based. Across six equivocal cases numerous other criteria were perceived to influence reimbursement policy. These included other considerations that stakeholders deemed crucial in this area, such as taking into account the cost to the patient, and managing crisis scenarios. However, negative impacts were also reported, in the form of bypassing regular procedures unnecessarily, dominance of an opinion leader, using information selectively, and influential conflicts of interest.Conclusions
‘Evidence’ and ‘negotiation’ are both essential inputs of reimbursement policy. Yet, purposely selected equivocal cases in Belgium provide a rich source to learn from and to improve the interaction between both. We formulated policy recommendations to reconcile the impact of all factors identified. A more systematic approach to reimburse new care may be one of many instruments to resolve the budgetary crisis in health care in other countries as well, by separating what is truly innovative and value for money from additional ‘waste’. 相似文献6.
Tefera Belachew David Lindstrom Abebe Gebremariam Dennis Hogan Carl Lachat Lieven Huybregts Patrick Kolsteren 《PloS one》2013,8(3)
Despite the high prevalence of adolescent food insecurity in Ethiopia, there is no study which documented its association with suboptimal dietary practices. The objective of this study is to determine the association between adolescent food insecurity and dietary practices. We used data on 2084 adolescents in the age group of 13–17 years involved in the first round survey of the five year longitudinal family study in Southwest Ethiopia. Adolescents were selected using residence stratified random sampling methods. Food insecurity was measured using scales validated in developing countries. Dietary practices were measured using dietary diversity score, food variety score and frequency of consuming animal source food. Multivariable regression models were used to compare dietary behaviors by food security status after controlling for socio-demographic and economic covariates.Food insecure adolescents had low dietary diversity score (P<0.001), low mean food variety score (P<0.001) and low frequency of consuming animal source foods (P<0.001). After adjusting for other variables in a multivariable logistic regression model, adolescent food insecurity (P<0.001) and rural residence (P<0.001) were negatively associated with the likelihood of having a diversified diet (P<0.001) and frequency of consuming animal source foods, while a high household income tertile was positively associated. Similarly, multivariable linear regression model showed that adolescent food insecurity was negatively associated with food variety score, while residence in semi-urban areas (P<0.001), in urban areas (P<0.001) and high household income tertile (P = 0.013) were positively associated. Girls were less likely to have diversified diet (P = 0.001) compared with boys.Our findings suggest that food insecurity has negative consequence on optimal dietary intake of adolescents. Food security interventions should look into ways of targeting adolescents to mitigate these dietary consequences and provide alternative strategies to improve dietary quality of adolescents in Southwest Ethiopia. 相似文献
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Alan Walton Elisabeth Stes Nicolas Cybulski Michiel Van Bel Sabrina I?igo Astrid Nagels Durand Evy Timmerman Jefri Heyman Laurens Pauwels Lieven De Veylder Alain Goossens Ive De Smet Frederik Coppens Sofie Goormachtig Kris Gevaert 《The Plant cell》2016,28(1):6-16
Ubiquitination, the covalent binding of the small protein modifier ubiquitin to a target protein, is an important and frequently studied posttranslational protein modification. Multiple reports provide useful insights into the plant ubiquitinome, but mostly at the protein level without comprehensive site identification. Here, we implemented ubiquitin combined fractional diagonal chromatography (COFRADIC) for proteome-wide ubiquitination site mapping on Arabidopsis thaliana cell cultures. We identified 3009 sites on 1607 proteins, thereby greatly increasing the number of known ubiquitination sites in this model plant. Finally, The Ubiquitination Site tool (http://bioinformatics.psb.ugent.be/webtools/ubiquitin_viewer/) gives access to the obtained ubiquitination sites, not only to consult the ubiquitination status of a given protein, but also to conduct intricate experiments aiming to study the roles of specific ubiquitination events. Together with the antibodies recognizing the ubiquitin remnant motif, ubiquitin COFRADIC represents a powerful tool to resolve the ubiquitination maps of numerous cellular processes in plants. 相似文献
8.
Leander A. H. Petersen Christian Lieven Subir K. Nandy John Villadsen Sten B. Jørgensen Ib Christensen Krist V. Gernaey 《Biotechnology and bioengineering》2019,116(11):2884-2895
The methanotrophic bacterium Methylococcus capsulatus is capable of assimilating methane and oxygen into protein-rich biomass, however, the diverse metabolism of the microorganism also allows for several undesired cometabolic side-reactions to occur. In this study, the ammonia cometabolism in Methylococcus capsulatus is investigated using pulse experiments. Surprisingly Methylococcus capsulatus oxidizes ammonia to nitrate through a yet unknown mechanism and fixes molecular nitrogen even at a high dissolved oxygen tension. The observed phenomena can be modeled using 14 ordinary differential equations and 18 kinetic parameters, of which 6 were revealed by Morris screening to be identifiable from the experimental data. Monte Carlo simulations showed that the model was robust and accurate even with uncertainty in the parameter values as confirmed by statistical error analysis. 相似文献
9.
Ormenese S de Almeida Engler J De Groodt R De Veylder L Inzé D Jacqmard A 《Annals of botany》2004,93(5):575-580
BACKGROUND AND AIMS: Kip-related-proteins (KRPs), negative regulators of cell division, have recently been discovered in plants but their in planta function is as yet unclear. In this study the spatial expression of all seven KRP genes in shoot apices of Arabidopsis thaliana were compared. METHODS: In situ hybridization analyses were performed on longitudinal sections of shoot apices from 2-month-old Arabidopsis plants. KEY RESULTS: The study provides evidence for different expression pattern groups. KRP1 and KRP2 expression is restricted to the endoreduplicating tissues. In contrast, KRP4 and KRP5 expression is mainly restricted to mitotically dividing cells. KRP3, KRP6 and KRP7 can be found in both mitotically dividing and endoreduplicating cells. CONCLUSION: The results suggest differential roles for the distinct KRPs. KRP1 and KRP2 might specifically be involved in the establishment of polyploidy. In contrast, KRP4 and KRP5 might be involved in regulating the progression through the mitotic cell cycle. KRP3, KRP6 and KRP7 might have a function in both types of cell cycle. 相似文献
10.
We investigated the synthesis of linked-ring DNAs by two DNA-ligation-based methods. In the first method, two DNA oligonucleotides were associated through a duplex segment of more than a full helical turn. Circularization of the entwined oligonucleotides by T4 DNA ligase resulted in two linked-ring DNAs with a total yield of approximately 40%. In the second method, a DNA oligonucleotide was circularized over a circular DNA template, resulting in the formation of approximately 10% linked-ring product. The circular nature of linked-ring DNAs was verified with exonuclease digestion and the existence of topological linkages was demonstrated by analyzing the electrophoretic mobility pattern of DNA products obtained from the digestion of each linked-ring DNA using specific restriction endonucleases. A linked-ring DNA library in which one of the two rings contained random-sequence nucleotides was also constructed and tested for compatibility with in vitro selection. 相似文献