Random Amplified Polymorphic DNA Technique: Technique that utilizes low-stringency polymerase chain reaction (PCR) amplification with single primers of arbitrary sequence to generate strain-specific arrays of anonymous DNA fragments. RAPD technique may be used to determine taxonomic identity, assess kinship relationships, analyze mixed genome samples, and create specific probes.DNA, Recombinant: Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.DNA Fingerprinting: A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
Random amplified polymorphic dna technique: Definition with Random amplified polymorphic dna ...Definition of Random amplified polymorphic dna technique with photos and pictures, translations, sample usage, and additional links for more information.
Microbiology Society Journals | Genetic diversity within Lactobacillus sakei and Lactobacillus curvatus and design of PCR...The genotypic and phenotypic diversity among isolates of the Lactobacillus curvatus/Lactobacillus graminis/Lactobacillus sakei group was evaluated by comparing RAPD data and results of biochemical tests, such as hydrolysis of arginine, D-lactate production, melibiose and xylose fermentation, and the presence of haem-dependent catalase. Analyses were applied to five type strains and to a collection of 165 isolates previously assigned to L. sakei or L. curvatus. Phenotypic and RAPD data were compared with each other and with previous DNA-DNA hybridization data. The phenotypic and genotypic separation between L. sakei, L. curvatus and L graminis was clear, and new insights into the detailed structure within L. sakei and L. curvatus were obtained. Individual strains could be typed by RAPD and, after the elimination of similar or identical isolates, two sub-groups in both L. curvatus and L. sakei were defined. The presence or absence of catalase activity further distinguished the ...
Analysis of genetic structure of Melia volkensii (Gurke.) populations using random amplified polymorphic DNA.Melia volkensii (Gurke.) is a popular fast growing agroforestry tree species in the East Africa's arid and semi arid lands (ASALs). The species is valued for its high quality termite resistant timber. In addition, its fruits are eaten by livestock thus making it the species of choice by small-scale farmers. However, the species has been overexploited and information on its existing gene pool is currently lacking. The present work was therefore carried out using random amplified polymorphic DNA (RAPD) markers to assess genetic diversity within and between populations in order to suggest appropriate conservation and management strategies. Eight RAPD primers generated 38 scorable polymorphic bands which were used to estimate genetic distances between populations and for construction of neighbour-joining phenograms. Analysis of Molecular Variance (AMOVA) indicated significant genetic differentiation between populations in the ...
Essential oil diversity and molecular characterization of Ephedra species using RAPD analysisBackground and objectives: The genus Ephedra (Ephedraceae) consists of about 40 species of mostly shrubs and rarely small trees around the world. In the present study, the essential oil (EO) diversity and genetic relationships were investigated in six Ephedra species from Iran using Random Amplified Polymorphic DNA (RAPD) markers. Methods: Theplants were collected from two different provinces; Azarbayjan (north-west) and Khorasan (north-east) of Iran. The EOs were obtained by hydro-distillation and analyzed by GC and GC/MS. The DNA was extracted from the aerial parts of the plants using a Qiagen Dneasy Plant Mini Kit. Amplification was performed using decamer RAPD primers. Results: A total of 187 bands were scored and used for the analysis of genetic distances. Genetic distance values ranged from 0.25 to 0.95.The analysis showed the highest genetic diversity (25%) between E. foliata with other species. Ephedra foliata formed ...
Quantitative strain-specific detection of Lactobacillus rhamnosus GG in human faecal samples by real-time PCR - Ahlroos - 2009 ...At the time we started to develop the strain-specific real-time PCR assay for L. rhamnosus GG we did not have the genome sequence on the basis of which the primers could have been designed. Instead, we chose to sequence a unique RAPD fragment of L. rhamnosus GG as the basis of the assay. Lactobacillus rhamnosus GG is a well-known probiotic marketed all over the world in dairy products and in capsules. Although more than 400 scientific studies on L. rhamnosus GG have been reported, the studies still go on actively. The real-time quantitative PCR method for L. rhamnosus GG was developed for clinical studies to avoid the laborious cultivation and characterization of bacterial isolates in faecal samples. Strain-specific PCR can be run straight from the DNA of mixed populations and quantification is also possible using real-time PCR.. The L. rhamnosus GG-specific primers designed were shown to amplify the PCR product only from the DNA of L. rhamnosus GG. The specificity of the ...
Biology: Genetic Diversity Using Random Amplified Polymorphic DNA (RAPD) Analysis for Aspergillus niger isolatesالمجلة العراقية للعلوم Iraqi Journal of Science A Refereed Science Journal Issued by the College of Science University of Baghdad Baghdad-Iraq. مجلة علمية محكمة تصدرها كلية العلوم- جامعة بغداد، بغداد- جمهورية العراق EISSN: 2312-1637 ISSN: 0067-2904
RAPD Variation in the Rare and Endangered Leucadendron Elimense (Proteaceae): Implications for Their Conservation. - Worcester...We measured genetic variation of the three rare sub-species of the cone bush, Leucadendron elimense (Proteaceae), in comparison with a widespread, common species, Leucadendron salignum, using randomly amplified polymorphic DNA (RAPDs). Despite small population sizes and restricted distributions, study populations of L. elimense showed high levels of genetic variation in all three sub-species (0.24-0.34) with a genetic variation of 0.35 for the species as a whole. This was slightly higher than that measured for L. salignum (0.30), the most ubiquitous species of Leucadendron in the Cape flora. Analysis of molecular variance (AMOVA) indicated that most of the genetic variation lay among individuals within populations. We suggest several mechanisms whereby high levels of genetic variation might persist in small, isolated populations of rare Cape Proteaceae and propose that such taxa can be protected in a series of very small reserves at ...
The Evolution of Vicia ramuliflora (Fabaceae) at Tetraploid and Diploid Levels Revealed with FISH and RAPDVicia ramuliflora L. is a widely distributed species in Eurasia with high economic value. For past 200 years, it has evolved a tetraploid cytotype and new subspecies at the diploid level. Based on taxonomy, cytogeography and other lines of evidence, previous studies have provided valuable information about the evolution of V. ramuliflora ploidy level, but due to the limited resolution of traditional methods, important questions remain. In this study, fluorescence in situ hybridization (FISH) and random amplified polymorphic DNA (RAPD) were used to analyze the evolution of V. ramuliflora at the diploid and tetraploid levels. Our aim was to reveal the genomic constitution and parents of the tetraploid V. ramuliflora and the relationships among diploid V. ramuliflora populations. Our study showed that the tetraploid cytotype of V. ramuliflora at Changbai Mountains (M) has identical 18S and 5S rDNA distribution patterns with the ...
Evaluation of diversity among Cynodon dactylon (L.) using RAPD markers. | Dr. Nematollah EtemadiAuthors: Nematollah Etemadi, Badraldin Ebrahim Sayed Tabatabei, Zabihollah Zamani, Jamshid Razmjoo, Ahmad Khalighi, Hossein Lessani Journal Title:Authors: Nematollah Etemadi, Badraldin Ebrahim Sayed Tabatabei, Zabihollah Zamani, Jamshid Razmjoo, Ahmad Khalighi, Hossein Lessani Journal Title: International Journal of Agriculture and Biology Volume 8 (2), Year 2006, Pages 198-202. Link to online resource: http://www.fspublishers.org/Issue.php?categoryID=32
Passion flower | History | Passion flowers | Passiflora OnlineHistory of the Passion flower Passiflora. The stunning flower and the Christian interpretation of its parts leading to it becoming widespread in Europe.
PlantFiles Pictures: Passiflora, Blue Passion Flower, Hardy Passion Flower, Passion Vine 'Blue Crown' (Passiflora caerulea) by...Welcome to the famous Dave's Garden website. Join our friendly community that shares tips and ideas for gardens, along with seeds and plants.
Browse by Journal - UnissResearchMarine Ecology Progress Series, Vol. 182 , p. 299-303. eISSN 1616-1599. Article.. Cossu, Piero and Maltagliati, Ferruccio and Lai, Tiziana and Casu, Marco and Curini Galletti, Marco and Castelli, Alberto (2012) Genetic structure of Hediste diversicolor (Polychaeta, Nereididae) from the north-western Mediterranean as revealed by DNA Inter-Simple Sequence Repeat (ISSR) markers. ...
Electron. J. Biotechnol. - vol.10 número3Extent and structure of genetic diversity in a collection of the tropical multipurpose shrub legume Cratylia argentea (Desv.) O. Kuntze as revealed by RAPD markers ...
بررسی چند شکلی ژنتیکی در ارقام گلرنگ با استفاده از نشانگرRAPDبه منظور بررسی چند شکلی ژنتیکی بین ارقام داخلی و خارجی گلرنگ با استفاده از نشانگر RAPD تعداد 20 رقم گلرنگ مورد بررسی قرار گرفت. در این آزمایش از 17 آغازگر10 نوکلئوتیدی استفاده شد و در نهایت تعداد 279 نوار قابل امتیاز-دهی ایجاد شد که 256 نوار در محدوده-ای بین 100 و 3000 جفت باز را شامل می-شد. نمودارهای حاصل از روش UPGMA ارقام را به چهار گروه اصلی تقسیم کرد. گروه اول دو رقم خارجی، و گروه دوم 2 رقم بومی داخلی و یک رقم اصلاح شده را شامل می-شد. گروه سوم ارقام زراعی محلی، ارقام وحشی و اصلاح شده را شامل می-شد. گروه چهارم نیز شامل دو رقم اصلاح شده ایرانی اصفهان و رقم KW4 بود. بیشترین
DNA Analysis: Traditional Techniques - DNA Analysis: Traditional Techniques | HowStuffWorksDNA Analysis: Traditional Techniques - Traditional DNA analysis techniques are explained in this section. Learn about traditional DNA analysis techniques.
Filter Tests | Friends of Water5.1.2 Chemical: The arithmetic average of the active agent of each test unit shall not exceed the MCL of the U.S. EPA Primary Drinking Water Regulations, or a similar standard established by any U.S. federal regulatory agency for materials not included in the U.S. EPA regulations. No single sample shall exceed the MCL by more than the established analytical error for the method used.. 5.2 Chemical Units: Chemical reduction shall be substantiated by tests showing compliance with the minimum requirements specified as follows:. 5.2.1 Chemical Reduction: Shall reduce the specified contaminant/s as shown in Table 1.. Complies. See Table 1.. Note: The results given in this table are the readings at 100 percent of manufacturer's listed capacity.. TABLE ONE. Concentration:. Chemical Concentration, Parts per million (mg/l). Input Water. Unit Output. Maximum Allowed. TTHM (as CHC13). 0.55. .002. ,0.1. Lead (as PbC12). 0.16. .000**. ,0.025. Fluoride. 8.00. 1.32. ,1.4 *****. Nitrate (as ...
How do you create a DNA fingerprint? | Reference.comCreating your own DNA fingerprint helps you to learn about DNA. This process takes about an hour to put together and overnight to set. You need a DNA sample, beakers, a laboratory, restriction...
The average (arithmetic mean) of a normal distribution of a : Problem Solving (PS)The average (arithmetic mean) of a normal distribution of a school's test scores is 65, and standard deviation of the distribution is 6.5. A student ...
Phylogenetic dendrogram of viral protein 4 (VP4) P a | Open-iPhylogenetic dendrogram of viral protein 4 (VP4) P and P rotaviruses at the amino acid level. Bootstraps values (1,000 replicates) |65% are shown. The
Identification and differentiation of Panax species using ELISA, RAPD and eastern blotting.Abstract Immunochemical and genetic methods have been developed in order to distinguish Panax spp. With the aim of establishing immunochemical methods, two hybridomas (3H4 and 5H8)..
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Why Parent Stress Can Impact Kids' DNAWhen parents are stressed out, even their kids' DNA is affected. A study found that adolescents had different DNA patterns depending on the degree of their parents' stress when the kids were in
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RAPD: RAPD (pronounced "rapid") stands for 'Random Amplified Polymorphic DNA'. It is a type of PCR reaction, but the segments of DNA that are amplified are random.Coles PhillipsSymmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Ligation-independent cloning: Ligation-independent cloning (LIC) is a form of molecular cloning that is able to be performed without the use of restriction endonucleases or DNA ligase. This allows genes that have restriction sites to be cloned without worry of chopping up the insert.List of strains of Escherichia coli: Escherichia coli is a well studied bacterium that was first identified by Theodor Escherich, after whom it was later named.Triparental mating: Triparental mating is a form of Bacterial conjugation where a conjugative plasmid present in one bacterial strain assists the transfer of a mobilizable plasmid present in a second bacterial strain into a third bacterial strain. Plasmids are introduced into bacteria for such purposes as transformation, cloning, or transposon mutagenesis.
(1/1307) Linear SRY transcript in equine testis.
Employing a combination of reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) techniques, the complete coding sequence of cDNA for the equine SRY gene was determined. We also attempted to make clear whether the equine SRY gene transcript is expressed in the adult testis, and whether the type of transcript is expressed as linear or circular RNA. As a result, in total a 1420 bp cDNA sequence was determined. Accomplishment of 3' RACE infers that equine SRY gene was expressed as a linear RNA transcript in testicular tissue just after puberty, in contrast to the situation in mice. (+info)
(2/1307) Molecular differentiation of Renibacterium salmoninarum isolates from worldwide locations.
Renibacterium salmoninarum is a genospecies that is an obligate pathogen of salmonid fish and is capable of intracellular survival. Conventional typing systems have failed to differentiate isolates of R. salmoninarum. We used two methods to assess the extent of molecular variation which was present in isolates from different geographic locations. In one analysis we investigated possible polymorphisms in a specific region of the genome, the intergenic spacer (ITS) region between the 16S and 23S rRNA genes. In the other analysis we analyzed differences throughout the genome by using randomly amplified polymorphic DNA (RAPD). We amplified the spacer region of 74 isolates by using PCR and performed a DNA sequence analysis with 14 geographically distinct samples. The results showed that the 16S-23S ribosomal DNA spacer region of R. salmoninarum is highly conserved and suggested that only a single copy of the rRNA operon is present in this slowly growing pathogen. DNA sequencing of the spacer region showed that it was the same length in all 14 isolates examined, and the same nucleotide sequence, sequevar 1, was obtained for 11 of these isolates. Two other sequevars were found. No tRNA genes were found. We found that RAPD analysis allows reproducible differentiation between isolates of R. salmoninarum obtained from different hosts and different geographic regions. By using RAPD analysis it was possible to differentiate between isolates with identical ITS sequences. (+info)
(3/1307) Randomly amplified polymorphic DNA analysis of clinical and environmental isolates of Vibrio vulnificus and other vibrio species.
Vibrio vulnificus is an estuarine bacterium that is capable of causing a rapidly fatal infection in humans. A randomly amplified polymorphic DNA (RAPD) PCR protocol was developed for use in detecting V. vulnificus, as well as other members of the genus Vibrio. The resulting RAPD profiles were analyzed by using RFLPScan software. This RAPD method clearly differentiated between members of the genus Vibrio and between isolates of V. vulnificus. Each V. vulnificus strain produced a unique band pattern, indicating that the members of this species are genetically quite heterogeneous. All of the vibrios were found to have amplification products whose sizes were within four common molecular weight ranges, while the V. vulnificus strains had an additional two molecular weight range bands in common. All of the V. vulnificus strains isolated from clinical specimens produced an additional band that was only occasionally found in environmental strains; this suggests that, as is the case with the Kanagawa hemolysin of Vibrio parahaemolyticus, the presence of this band may be correlated with the ability of a strain to produce an infection in humans. In addition, band pattern differences were observed between encapsulated and nonencapsulated isogenic morphotypes of the same strain of V. vulnificus. (+info)
(4/1307) A randomly amplified polymorphic DNA marker specific for the Bacillus cereus group is diagnostic for Bacillus anthracis.
Aiming to develop a DNA marker specific for Bacillus anthracis and able to discriminate this species from Bacillus cereus, Bacillus thuringiensis, and Bacillus mycoides, we applied the randomly amplified polymorphic DNA (RAPD) fingerprinting technique to a collection of 101 strains of the genus Bacillus, including 61 strains of the B. cereus group. An 838-bp RAPD marker (SG-850) specific for B. cereus, B. thuringiensis, B. anthracis, and B. mycoides was identified. This fragment included a putative (366-nucleotide) open reading frame highly homologous to the ypuA gene of Bacillus subtilis. The restriction analysis of the SG-850 fragment with AluI distinguished B. anthracis from the other species of the B. cereus group. (+info)
(5/1307) Class I integrons in Gram-negative isolates from different European hospitals and association with decreased susceptibility to multiple antibiotic compounds.
Class I integrons are associated with carriage of genes encoding resistance to antibiotics. Expression of inserted resistance genes within these structures can be poor and, as such, the clinical relevance in terms of the effect of integron carriage on susceptibility has not been investigated. Of 163 unrelated Gram-negative isolates randomly selected from the intensive care and surgical units of 14 different hospitals in nine European countries, 43.0% (70/163) of isolates were shown to be integron-positive, with inserted gene cassettes of various sizes. Integrons were detected in isolates from all hospitals with no particular geographical variations. Integron-positive isolates were statistically more likely to be resistant to aminoglycoside, quinolone and beta8-lactam compounds, including third-generation cephalosporins and monobactams, than integron-negative isolates. Integron-positive isolates were also more likely to be multi-resistant than integron-negative isolates. This association implicates integrons in multi-drug resistance either directly through carriage of specific resistance genes, or indirectly by virtue of linkage to other resistance determinants such as extended-spectrum beta-lactamase genes. As such their widespread presence is a cause for concern. There was no association between the presence of integrons and susceptibility to cefepime, amikacin and the carbapenems, to which at least 97% of isolates were fully susceptible. (+info)
(6/1307) Use of molecular subtyping to document long-term persistence of Corynebacterium diphtheriae in South Dakota.
Enhanced surveillance of patients with upper respiratory symptoms in a Northern Plains community revealed that approximately 4% of them were infected by toxigenic Corynebacterium diphtheriae of both mitis and gravis biotypes, showing that the organism is still circulating in the United States. Toxigenic C. diphtheriae was isolated from five members of four households. Four molecular subtyping methods-ribotyping, multilocus enzyme electrophoresis (MEE), random amplified polymorphic DNA (RAPD), and single-strand conformation polymorphism-were used to molecularly characterize these strains and compare them to 17 archival South Dakota strains dating back to 1973 through 1983 and to 5 isolates collected from residents of diverse regions of the United States. Ribotyping and RAPD clearly demonstrated the household transmission of isolates and provided precise information on the circulation of several distinct strains within three households. By MEE, most recent and archival South Dakota strains were identified as closely related and clustered within the newly identified ET (electrophoretic type) 215 complex. Furthermore, three recent South Dakota isolates and eight archival South Dakota isolates were indistinguishable by both ribotyping and RAPD. All of these molecular methods showed that recent South Dakota isolates and archival South Dakota isolates were more closely related to each other than to the C. diphtheriae strains isolated in other parts of the United States or worldwide. The data also supported the improbability of importation of C. diphtheriae into this area and rather strongly suggest the long-term persistence of the organism in this region. (+info)
(7/1307) Isolation and characterization of a novel promoter for the bovine growth hormone receptor gene.
The use of alternative promoters represents an important mechanism for the regulation of growth hormone receptor (GHR) gene expression. Two promoters have been isolated previously for the GHR gene: the P1 promoter that drives liver-specific expression, and the P2 promoter that drives ubiquitous expression. In the present study, we isolated a third GHR promoter termed P3. The P3 promoter was GC-rich and TATA-less. The P3 promoter was able to drive the expression of a luciferase reporter gene in cell lines Hep G2, PLC/PRF/5, and BHK-21. In vivo, the P3 promoter initiated transcription from two major sites in exon 1C of the GHR gene in many tissues. In the adult bovine liver, the P3-transcribed GHR mRNA represented only 10% of the total GHR mRNA pool. In non-hepatic tissues such as kidney, skeletal muscle, mammary gland, and uterus, P3-transcribed GHR mRNA represented 30-40% of the total GHR mRNA pool. Within the bovine GHR gene, the P3 promoter was located immediately downstream from the P2 promoter. In transfected cells, the P2 promoter served as an enhancer for the P3 promoter. Existence and co-regulation of two ubiquitous promoters may be a mechanism for achieving a high level of expression of the GHR gene in multiple tissues. (+info)
(8/1307) Identification of a glucose response element in the promoter of the rat glucagon receptor gene.
We cloned the 5' upstream region of the rat glucagon receptor gene, demonstrating that the 5' noncoding domain of the glucagon receptor mRNA contained two untranslated exons of 131 and 166 nucleotides (nt), respectively, separated by two introns of 0.6 and 3.2 kilobase pairs. We also observed an alternative splicing involving the 166-base pair exon. Cloning of up to 2 kilobase pairs of the newly identified genomic domain and transfection of various constructs driving a reporter gene, in pancreatic islet cell line INS-1, uncovered a strong glucose regulation of the promoter activity of plasmids containing up to nucleotide -868, or more, upstream from the transcriptional start point. This promoter activity displayed threshold-like behavior, with low activity of the promoter below 5 mM glucose, and maximal activation as of 10 mM glucose. This glucose regulation was mapped to a highly palindromic 19-nucleotide region between nt -545 and -527. Indeed, deletion or mutation of this sequence abolished the glucose regulation. This domain contained two palindromic "E-boxes" CACGTG and CAGCTG separated by 3 nt, a feature similar to the "L4 box" found in the pyruvate kinase L gene promoter. This is the first description of a G protein-coupled receptor gene promoter regulated by glucose. (+info)