Functional domains of a T-DNA promoter active in crown gall tumors

1987 ◽  
Vol 7 (1) ◽  
pp. 59-67
Author(s):  
W B Bruce ◽  
W B Gurley
Keyword(s):  
Promoter Activity ◽  
Large Scale ◽  
Transcriptional Activity ◽  
Transcriptional Start Site ◽  
Internal Standard ◽  
Significant Loss ◽  
Internal Deletion ◽  
Substitution Mutations ◽  
Tata Motif ◽  
A Minor

Promoter domains required for transcriptional expression of the 780 gene of T-right (pTi15955) were identified by deletion mutagenesis. Accurate quantitation of transcriptional activity of a series of 5' and internal deletion mutants was achieved by using a double gene vector containing a reference 780 gene as an internal standard. Results of the 5' deletions delineated an activator element located between -440 and -229 base pairs (bp) from the start of transcription. Removal of this region resulted in a 100-fold decrease in promoter activity. Two relatively small internal deletion/substitution mutations at positions -74 to -76 and -98 to -112 reduced promoter activity to 38 and 42%, respectively. In most cases large-scale internal deletions (38 to 151 bp) occurring in various locations from positions -12 to -348 bp caused a significant loss in major promoter activity. However, three internal deletions starting at position -37 and extending upstream as far as -153 bp either had little effect on transcriptional activity or resulted in increased activity. Removal of the TATA motif drastically reduced promoter activity to less than 0.1% of the wild type. A minor start of transcription was detected 60 bases upstream from the major transcriptional start site. This minor promoter shares the same activator element as the major promoter for full activity. Deletion and insertion mutations downstream of the minor promoter TATA demonstrated the role of the TATA box in positioning the start of transcription.

scholarly journals Functional domains of a T-DNA promoter active in crown gall tumors.

1987 ◽  
Vol 7 (1) ◽  
pp. 59-67 ◽  
Author(s):  
W B Bruce ◽  
W B Gurley
Keyword(s):  
Promoter Activity ◽  
Large Scale ◽  
Transcriptional Activity ◽  
Transcriptional Start Site ◽  
Internal Standard ◽  
Significant Loss ◽  
Internal Deletion ◽  
Substitution Mutations ◽  
Tata Motif ◽  
A Minor

Promoter domains required for transcriptional expression of the 780 gene of T-right (pTi15955) were identified by deletion mutagenesis. Accurate quantitation of transcriptional activity of a series of 5' and internal deletion mutants was achieved by using a double gene vector containing a reference 780 gene as an internal standard. Results of the 5' deletions delineated an activator element located between -440 and -229 base pairs (bp) from the start of transcription. Removal of this region resulted in a 100-fold decrease in promoter activity. Two relatively small internal deletion/substitution mutations at positions -74 to -76 and -98 to -112 reduced promoter activity to 38 and 42%, respectively. In most cases large-scale internal deletions (38 to 151 bp) occurring in various locations from positions -12 to -348 bp caused a significant loss in major promoter activity. However, three internal deletions starting at position -37 and extending upstream as far as -153 bp either had little effect on transcriptional activity or resulted in increased activity. Removal of the TATA motif drastically reduced promoter activity to less than 0.1% of the wild type. A minor start of transcription was detected 60 bases upstream from the major transcriptional start site. This minor promoter shares the same activator element as the major promoter for full activity. Deletion and insertion mutations downstream of the minor promoter TATA demonstrated the role of the TATA box in positioning the start of transcription.

scholarly journals Murine Macrophage Mannose Receptor Promoter Is Regulated by the Transcription Factors PU.1 and SP1

Blood ◽  
1997 ◽  
Vol 90 (10) ◽  
pp. 4135-4143 ◽  
Author(s):  
Quentin Eichbaum ◽  
David Heney ◽  
David Raveh ◽  
Michael Chung ◽  
Mark Davidson ◽  
...  
Keyword(s):  
Binding Sites ◽  
Promoter Activity ◽  
Transcriptional Activity ◽  
Transmembrane Protein ◽  
Transcriptional Start Site ◽  
Mannose Receptor ◽  
Luciferase Reporter ◽  
Start Site ◽  
Luciferase Reporter Gene ◽  
Wide Range

Abstract The mannose receptor (MR) is a transmembrane protein that functions primarily as a phagocytic receptor for a wide range of microorganisms. Its expression appears to be restricted to tissue macrophages and Langerhans cells. To gain an understanding of the regulation of the gene, we have isolated the 5′ flanking sequence of the murine MR gene and have analyzed a 536-bp sequence upstream of the ATG start site for transcriptional activity. This sequence lacks a TATA box but contains an initiator (Inr) consensus element overlapping the single transcriptional start site. Transcription factor binding sites contained within this sequence include PU.1, Sp1, ETS, GATA, and MYB motifs. Serial 100-bp deletions of this promoter fragment fused to a luciferase reporter gene showed various patterns of activity when transfected into different cell types. In myeloid cells, sequence elements upstream of bp −300 appeared to have a silencing effect on promoter activity. Of the four potential PU.1 binding sites contained within the fragment, one site (at −164) bound the PU.1 factor most strongly, whereas the adjacent PU.1 site (at −177 bp) bound PU.1 to a lesser degree. Mutations of these sites decreased transcriptional activity but did not abolish it. However, promoter activity was abrogated when both the −164 bp PU.1 site and the adjacent −177 bp PU.1 site were mutated. In addition, mutation of the Sp1 site also significantly reduced promoter activity. Cotransfection studies in Drosophila Schneider cells indicated that PU.1 and Sp1 may function synergistically in transactivating the murine MR. This study indicates that MR gene expression is regulated in part by the interaction between the ubiquitously expressed factor Sp1 and the lymphoid/myeloid factor PU.1 and provides a basis for studying the regulation of this gene.

Interference mitigation in point to point wireless sensor networks using LSP protocol and time division multiplexing approach

2020 ◽  
Vol 39 (4) ◽  
pp. 5449-5458
Author(s):  
A. Arokiaraj Jovith ◽  
S.V. Kasmir Raja ◽  
A. Razia Sulthana
Keyword(s):  
Energy Consumption ◽  
Large Scale ◽  
Control Parameter ◽  
Interference Mitigation ◽  
Wireless Sensor ◽  
Point To Point ◽  
A Minor ◽  
Two Stages ◽  
Time Division ◽  
And Control

Interference in Wireless Sensor Network (WSN) predominantly affects the performance of the WSN. Energy consumption in WSN is one of the greatest concerns in the current generation. This work presents an approach for interference measurement and interference mitigation in point to point network. The nodes are distributed in the network and interference is measured by grouping the nodes in the region of a specific diameter. Hence this approach is scalable and isextended to large scale WSN. Interference is measured in two stages. In the first stage, interference is overcome by allocating time slots to the node stations in Time Division Multiple Access (TDMA) fashion. The node area is split into larger regions and smaller regions. The time slots are allocated to smaller regions in TDMA fashion. A TDMA based time slot allocation algorithm is proposed in this paper to enable reuse of timeslots with minimal interference between smaller regions. In the second stage, the network density and control parameter is introduced to reduce interference in a minor level within smaller node regions. The algorithm issimulated and the system is tested with varying control parameter. The node-level interference and the energy dissipation at nodes are captured by varying the node density of the network. The results indicate that the proposed approach measures the interference and mitigates with minimal energy consumption at nodes and with less overhead transmission.

scholarly journals Flavonoid-Modifying Capabilities of the Human Gut Microbiome—An In Silico Study

Nutrients ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 2688
Author(s):  
Tobias Goris ◽  
Rafael R. C. Cuadrat ◽  
Annett Braune
Keyword(s):  
Gut Microbiome ◽  
Large Scale ◽  
Health Impact ◽  
Gut Bacteria ◽  
Human Gut ◽  
Positive Health ◽  
Human Gut Microbiome ◽  
Nutritional Recommendations ◽  
Genes Encoding ◽  
A Minor

Flavonoids are a major group of dietary plant polyphenols and have a positive health impact, but their modification and degradation in the human gut is still widely unknown. Due to the rise of metagenome data of the human gut microbiome and the assembly of hundreds of thousands of bacterial metagenome-assembled genomes (MAGs), large-scale screening for potential flavonoid-modifying enzymes of human gut bacteria is now feasible. With sequences of characterized flavonoid-transforming enzymes as queries, the Unified Human Gastrointestinal Protein catalog was analyzed and genes encoding putative flavonoid-modifying enzymes were quantified. The results revealed that flavonoid-modifying enzymes are often encoded in gut bacteria hitherto not considered to modify flavonoids. The enzymes for the physiologically important daidzein-to-equol conversion, well studied in Slackiaisoflavoniconvertens, were encoded only to a minor extent in Slackia MAGs, but were more abundant in Adlercreutzia equolifaciens and an uncharacterized Eggerthellaceae species. In addition, enzymes with a sequence identity of about 35% were encoded in highly abundant MAGs of uncultivated Collinsella species, which suggests a hitherto uncharacterized daidzein-to-equol potential in these bacteria. Of all potential flavonoid modification steps, O-deglycosylation (including derhamnosylation) was by far the most abundant in this analysis. In contrast, enzymes putatively involved in C-deglycosylation were detected less often in human gut bacteria and mainly found in Agathobacter faecis (formerly Roseburia faecis). Homologs to phloretin hydrolase, flavanonol/flavanone-cleaving reductase and flavone reductase were of intermediate abundance (several hundred MAGs) and mainly prevalent in Flavonifractor plautii. This first comprehensive insight into the black box of flavonoid modification in the human gut highlights many hitherto overlooked and uncultured bacterial genera and species as potential key organisms in flavonoid modification. This could lead to a significant contribution to future biochemical-microbiological investigations on gut bacterial flavonoid transformation. In addition, our results are important for individual nutritional recommendations and for biotechnological applications that rely on novel enzymes catalyzing potentially useful flavonoid modification reactions.

scholarly journals Investigation of the Wilson gene ATP7B transcriptional start site and the effect of core promoter alterations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Clemens Höflich ◽  
Angela Brieger ◽  
Stefan Zeuzem ◽  
Guido Plotz
Keyword(s):  
Wilson Disease ◽  
Transcription Initiation ◽  
Transcriptional Activity ◽  
Core Promoter ◽  
Transcriptional Start Site ◽  
Copper Metabolism ◽  
Biologically Relevant ◽  
The Core ◽  
Translational Start

AbstractPathogenic genetic variants in the ATP7B gene cause Wilson disease, a recessive disorder of copper metabolism showing a significant variability in clinical phenotype. Promoter mutations have been rarely reported, and controversial data exist on the site of transcription initiation (the core promoter). We quantitatively investigated transcription initiation and found it to be located in immediate proximity of the translational start. The effects human single-nucleotide alterations of conserved bases in the core promoter on transcriptional activity were moderate, explaining why clearly pathogenic mutations within the core promoter have not been reported. Furthermore, the core promoter contains two frequent polymorphisms (rs148013251 and rs2277448) that could contribute to phenotypical variability in Wilson disease patients with incompletely inactivating mutations. However, neither polymorphism significantly modulated ATP7B expression in vitro, nor were copper household parameters in healthy probands affected. In summary, the investigations allowed to determine the biologically relevant site of ATP7B transcription initiation and demonstrated that genetic variations in this site, although being the focus of transcriptional activity, do not contribute significantly to Wilson disease pathogenesis.

scholarly journals TreeMerge: a new method for improving the scalability of species tree estimation methods

2019 ◽  
Vol 35 (14) ◽  
pp. i417-i426 ◽  
Author(s):  
Erin K Molloy ◽  
Tandy Warnow
Keyword(s):  
Large Scale ◽  
Species Tree ◽  
New Method ◽  
Divide And Conquer ◽  
Supplementary Information ◽  
Estimation Methods ◽  
Running Time ◽  
Tree Estimation ◽  
Computationally Intensive ◽  
A Minor

Abstract Motivation At RECOMB-CG 2018, we presented NJMerge and showed that it could be used within a divide-and-conquer framework to scale computationally intensive methods for species tree estimation to larger datasets. However, NJMerge has two significant limitations: it can fail to return a tree and, when used within the proposed divide-and-conquer framework, has O(n5) running time for datasets with n species. Results Here we present a new method called ‘TreeMerge’ that improves on NJMerge in two ways: it is guaranteed to return a tree and it has dramatically faster running time within the same divide-and-conquer framework—only O(n2) time. We use a simulation study to evaluate TreeMerge in the context of multi-locus species tree estimation with two leading methods, ASTRAL-III and RAxML. We find that the divide-and-conquer framework using TreeMerge has a minor impact on species tree accuracy, dramatically reduces running time, and enables both ASTRAL-III and RAxML to complete on datasets (that they would otherwise fail on), when given 64 GB of memory and 48 h maximum running time. Thus, TreeMerge is a step toward a larger vision of enabling researchers with limited computational resources to perform large-scale species tree estimation, which we call Phylogenomics for All. Availability and implementation TreeMerge is publicly available on Github (http://github.com/ekmolloy/treemerge). Supplementary information Supplementary data are available at Bioinformatics online.

The nuclear orphan receptors COUP-TFII and Ear-2 act as silencers of the human oxytocin gene promoter

1997 ◽  
Vol 19 (2) ◽  
pp. 163-172 ◽  
Author(s):  
K Chu ◽  
HH Zingg
Keyword(s):  
Receptor Binding ◽  
Promoter Activity ◽  
Transcriptional Activity ◽  
Gene Promoter ◽  
Fine Tuning ◽  
Orphan Receptor ◽  
Expression Vectors ◽  
Mobility Shift ◽  
Interaction Sites

We have previously shown that COUP-TFII and Ear-2, two members of the nuclear orphan receptor family, are able to repress oestrogen-stimulated transcriptional activity of the human oxytocin (OT) gene promoter by binding to a site that overlaps with the oestrogen response element (ERE) present in the 5' flanking region of the gene. Although most nuclear receptor-mediated transcriptional repression conforms with the paradigm of passive repression and involves competitive binding to an activator site, active repression, i.e. silencing of basal promoter activity, has been observed in a limited number of cases. Here we show by co-transfection experiments using COUP-TFII and Ear-2 expression vectors and reporter constructs containing OT gene promoter fragments linked to the chloramphenicol acetyltransferase gene that both COUP-TFII and Ear-2 are capable of silencing basal OT gene promoter activity by 54 and 75% respectively. 5' Deletion and footprint analyses revealed two areas of functionally important interaction sites: (1) a direct TGACC(T/C) repeat overlapping the ERE and (2) a more promoter-proximal area centred at - 90 containing three imperfect direct repeats (R1-R3) spaced by four nucleotides each. Mutagenesis of reporter constructs as well as electrophoretic mobility-shift assays demonstrated that each of the three proximal repeats R1-R3 contributed to orphan receptor binding and the silencing effect. Inasmuch as the orphan receptor-binding sites are not involved in mediating basal transcriptional activity of the OT gene promoter, the observed effects are best interpreted as active repression or promoter silencing. Moreover, since COUP-TFII and Ear-2 are both co-expressed in OT-expressing uterine epithelial cells, the novel transcriptional effects described here are likely to be of functional importance in the fine-tuning of uterine OT gene expression in vivo.

XBP-1 increases ERα transcriptional activity through regulation of large-scale chromatin unfolding

2004 ◽  
Vol 323 (1) ◽  
pp. 269-274 ◽  
Author(s):  
Yan Fang ◽  
Jinghua Yan ◽  
Lihua Ding ◽  
Yufei Liu ◽  
Jianhua Zhu ◽  
...  
Keyword(s):  
Large Scale ◽  
Transcriptional Activity

CLIL theory and empirical reality – Two sides of the same coin?

2017 ◽  
Vol 5 (1) ◽  
pp. 110-134 ◽  
Author(s):  
Dominik Rumlich
Keyword(s):  
Large Scale ◽  
Self Concept ◽  
Empirical Reality ◽  
Longitudinal Model ◽  
Composition Effects ◽  
Class Composition ◽  
Quasi Experimental ◽  
Individual Variables ◽  
Conducting Research ◽  
A Minor

This article summarizes the essential theoretical and empirical findings of a large-scale doctoral dissertation study on content and language integrated learning (CLIL) streams at German secondary schools (Gymnasium) with up to three content subjects taught in English (Rumlich, 2016). A theoretical account rooted in teaching English as a foreign language (EFL), language acquisition and educational psychology provides the basis for the development of a comprehensive longitudinal model of general EFL proficiency, which incorporates cognitive, affective-motivational, and further individual variables. In a second step, the model is used to estimate the effects of CLIL on general EFL proficiency, EFL self-concept and interest over a span of two school years (Year 6 to Year 8). The statistical evaluation of the quasi-experimental data from 1,000 learners finds large initial differences prior to CLIL due to selection, preparation, and class composition effects brought about by the implementation of CLIL within streams. After two years, the analyses found no CLIL-related benefits for general EFL proficiency or interest in EFL classes and solely a minor increase in EFL self-concept that might be attributable to CLIL. The results make a strong claim for comprehensive longitudinal model-based evaluations and the inclusion of selection, preparation, and class composition effects when conducting research on CLIL programmes in similar settings. The findings also suggest that not all language competences and affective-motivational dispositions might benefit from CLIL (the way it is currently taught in Germany) to the same extent.

scholarly journals Energy release and conversion by reconnection in the magnetotail

2005 ◽  
Vol 23 (10) ◽  
pp. 3365-3373 ◽  
Author(s):  
J. Birn ◽  
M. Hesse
Keyword(s):  
Energy Transfer ◽  
Energy Release ◽  
Large Scale ◽  
Magnetic Energy ◽  
Minor Role ◽  
Ohmic Dissipation ◽  
Particle Simulations ◽  
Minor Part ◽  
Reconnection Site ◽  
A Minor

Abstract. Magnetic reconnection is the crucial process in the release of magnetic energy previously stored in the magnetotail in association with substorms. However, energy transfer and dissipation in the vicinity of the reconnection site is only a minor part of the energy conversion. We discuss the energy release, transport, and conversion based on large-scale resistive MHD simulations of magnetotail dynamics and more localized full particle simulations of reconnection. We address in particular, where the energy is released, how it propagates and where and how it is converted from one form into another. We find that Joule (or ohmic) dissipation plays only a minor role in the overall energy transfer. Bulk kinetic energy, although locally significant in the outflow from the reconnection site, plays a more important role as mediator or catalyst in the transfer between magnetic and thermal energy. Generator regions with potential auroral consequences are located primarily off the equatorial plane in the boundary regions of the plasma sheet.

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