The Experts below are selected from a list of 637701 Experts worldwide ranked by ideXlab platform
Swati Patankar - One of the best experts on this subject based on the ideXlab platform.
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Upstream AUGs and Upstream ORFs can regulate the downstream ORF in Plasmodium falciparum.
Malaria journal, 2015Co-Authors: Mayank Kumar, Vivek Srinivas, Swati PatankarAbstract:Background Upstream open reading frames (uORFs) and Upstream AUGs (uAUGs) can regulate the translation of downstream ORFs. The AT rich genome of Plasmodium falciparum, due to the higher AT content of start and stop codons, has the potential to give rise to a large number of uORFs and uAUGs that may affect expression of their flanking ORFs.
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Upstream AUGs and Upstream ORFs can regulate the downstream ORF in Plasmodium
2015Co-Authors: Vivek Srinivas, Swati PatankarAbstract:Background: Upstream open reading frames (uORFs) and Upstream AUGs (uAUGs) can regulate the translation of downstream ORFs. The AT rich genome of Plasmodium falciparum, due to the higher AT content of start and stop codons, has the potential to give rise to a large number of uORFs and uAUGs that may affect expression of their flank ing ORFs. Methods: A bioinformatics approach was used to detect uATGs associated with different genes in the parasite. To study the effect of some of these uAUGs on the expression of the downstream ORF, promoters and 5 ′ leaders containing uAUGs and uORFs were cloned Upstream of a luciferase reporter gene. Luciferase assays were carried out in transient transfection experiments to assess the effects of uAUGs and mutations on reporter expression. Results: The average number of uATGs and uORFs seen in P. falciparum coding sequences (CDS) is expectedly high compared to other less biased genomes. Certain genes, including the var gene family contain the maximum number of uATGs and uORFs in the parasite. They possess ~5 times more uORFs and ~4.5 times more uAUGs within 100 bases Upstream of the start codons than other CDS of the parasite. A 60 bp Upstream region containing three ORFs and five ATGs from var gene PF3D7_0400100 and a gene of unknown function (PF3D7_0517100) when cloned Upstream of the luciferase start codon, driven by the hsp86 promoter, resulted in loss of luciferase activity. This was restored when all the ATGs present in the −60 bp were mutated to TTGs. Point mutations in the ATGs showed that even one AUG was sufficient to repress the luciferase gene. Conclusions: Overall, this work indicates that the P. falciparum genome has a large number of uATGs and uORFs that can repress the expression of flanking ORFs. The role of AUGs in translation initiation suggests that this repression is mediated by preventing the translation initiation complex from reaching the main AUG of the downstream ORF. How the P. falciparum ribosome is able to bypass these uAUGs and uORFs for highly expressed genes remains a question for future research.
Mark W. Denny - One of the best experts on this subject based on the ideXlab platform.
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A biomechanical hypothesis explaining Upstream movements by the freshwater snail Elimia
Functional Ecology, 1997Co-Authors: A. D. Huryn, Mark W. DennyAbstract:1. Many taxa of freshwater invertebrates show active Upstream movements, particularly the snails. Hypotheses explaining this behaviour invoke the search for food or space, compensation for drift, avoidance of predation and hydrodynamic effects. The pervasiveness of Upstream movements among remote lineages of snails (two subclasses, three orders, 10 families), however, suggests that snails may move Upstream for mechanical rather than adaptive reasons. 2. It is proposed that Upstream movements by snails are a function of torque on the snail’s foot generated by hydrodynamic drag on the shell. When subject to high broadside drag-forces on their shells, snails are able to reduce torque and stabilize orientation only by directing their anterior aspect Upstream. 3. Movements of the freshwater pleurocerid snail Elimia were studied by following marked free-ranging individuals in six streams in Alabama, USA (four species, eight populations). 4. Populations showed either no net movement (two streams) or significant Upstream movements ranging to a mean of ≈40 m over a 3-month period (four streams). Movement patterns were stream specific rather than species or population specific. Within populations showing significant Upstream movements, snails with shell lengths ≤10 mm showed little net movement. Larger snails showed movements from 0 to >200 m Upstream. 5. A torque-constrained random walk model was used to perform a post hoc test of the hypothesis that Upstream movements were a function of torque on the snail’s foot generated by hydrodynamic drag on the shell. The model predicted Upstream and size-dependent movement patterns that approximated those observed for snails in the field.
Mayank Kumar - One of the best experts on this subject based on the ideXlab platform.
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Upstream AUGs and Upstream ORFs can regulate the downstream ORF in Plasmodium falciparum.
Malaria journal, 2015Co-Authors: Mayank Kumar, Vivek Srinivas, Swati PatankarAbstract:Background Upstream open reading frames (uORFs) and Upstream AUGs (uAUGs) can regulate the translation of downstream ORFs. The AT rich genome of Plasmodium falciparum, due to the higher AT content of start and stop codons, has the potential to give rise to a large number of uORFs and uAUGs that may affect expression of their flanking ORFs.
Vivek Srinivas - One of the best experts on this subject based on the ideXlab platform.
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Upstream AUGs and Upstream ORFs can regulate the downstream ORF in Plasmodium falciparum.
Malaria journal, 2015Co-Authors: Mayank Kumar, Vivek Srinivas, Swati PatankarAbstract:Background Upstream open reading frames (uORFs) and Upstream AUGs (uAUGs) can regulate the translation of downstream ORFs. The AT rich genome of Plasmodium falciparum, due to the higher AT content of start and stop codons, has the potential to give rise to a large number of uORFs and uAUGs that may affect expression of their flanking ORFs.
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Upstream AUGs and Upstream ORFs can regulate the downstream ORF in Plasmodium
2015Co-Authors: Vivek Srinivas, Swati PatankarAbstract:Background: Upstream open reading frames (uORFs) and Upstream AUGs (uAUGs) can regulate the translation of downstream ORFs. The AT rich genome of Plasmodium falciparum, due to the higher AT content of start and stop codons, has the potential to give rise to a large number of uORFs and uAUGs that may affect expression of their flank ing ORFs. Methods: A bioinformatics approach was used to detect uATGs associated with different genes in the parasite. To study the effect of some of these uAUGs on the expression of the downstream ORF, promoters and 5 ′ leaders containing uAUGs and uORFs were cloned Upstream of a luciferase reporter gene. Luciferase assays were carried out in transient transfection experiments to assess the effects of uAUGs and mutations on reporter expression. Results: The average number of uATGs and uORFs seen in P. falciparum coding sequences (CDS) is expectedly high compared to other less biased genomes. Certain genes, including the var gene family contain the maximum number of uATGs and uORFs in the parasite. They possess ~5 times more uORFs and ~4.5 times more uAUGs within 100 bases Upstream of the start codons than other CDS of the parasite. A 60 bp Upstream region containing three ORFs and five ATGs from var gene PF3D7_0400100 and a gene of unknown function (PF3D7_0517100) when cloned Upstream of the luciferase start codon, driven by the hsp86 promoter, resulted in loss of luciferase activity. This was restored when all the ATGs present in the −60 bp were mutated to TTGs. Point mutations in the ATGs showed that even one AUG was sufficient to repress the luciferase gene. Conclusions: Overall, this work indicates that the P. falciparum genome has a large number of uATGs and uORFs that can repress the expression of flanking ORFs. The role of AUGs in translation initiation suggests that this repression is mediated by preventing the translation initiation complex from reaching the main AUG of the downstream ORF. How the P. falciparum ribosome is able to bypass these uAUGs and uORFs for highly expressed genes remains a question for future research.
Stéphane Lemarié - One of the best experts on this subject based on the ideXlab platform.
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Downstream labeling and Upstream price competition
European Economic Review, 2012Co-Authors: Olivier Bonroy, Stéphane LemariéAbstract:This paper analyses the economic consequences of labeling in a setting with two vertically related markets. Labeling on the downstream market affects Upstream price competition through two effects: a differentiation effect and a ranking effect. The magnitude of these two effects determines who in the supply chain will receive the benefits and who will bear the burden of labeling. For instance, whenever the ranking effect dominates the differentiation effect, the low-quality Upstream firm loses from labeling while all downstream actors are individually better off. By decreasing the low-quality input price, the label acts as a subsidy and leads to an increase of the downstream market welfare. This analysis furthers our understanding of the economic consequences of labeling in cases like those of GMOs or restaurants.
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Downstream labeling and Upstream price competition
2010Co-Authors: Olivier Bonroy, Stéphane LemariéAbstract:The paper analyses the economic consequences of labeling in a setting with two vertically related markets. Labeling on the downstream market affects Upstream price competition through two effects : a differentiation effect and a ranking effect. The magnitude of these two effects determines who in the supply chain will receive the benefits and who will bear the burden of labeling. For instance, whenever the ranking effect dominates the differentiation effect, the low quality Upstream firm loses from labeling while all downstream actors are individually better off. By decreasing the low quality input price, the label acts then as a subsidy which assures an increase of the downstream market welfare. This analysis furthers our understanding of the economic consequences of the public labeling in cases like restaurants or GMOs.
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Upstream Competition and Downstream Labelling
2008Co-Authors: Olivier Bonroy, Stéphane LemariéAbstract:This paper analyses the impact of labelling in a context where the products come from a rather long supply chain. We consider a case where there is an information problem about the product quality in the downstream part of the chain, but not in the Upstream part. We show that the implementation of a label to solve this information problem affects the competition in the Upstream part of the chain. In particular, competition may be soften up to a point where both the high and the low quality Upstream suppliers both benefit from labelling while all the intermediary producers or final consumers loose from labelling. This result is established on the basis of a simple model with two vertically related markets (a competitive downstream market which is supplied by an Upstream duopoly) and where the quality of the output downstream is determined by the quality of the input Upstream. This analysis is informative to understand the impact of labelling in different cases concerning the agricultural sector (poultry meat, GMOs).
