scholarly journals Fragment Size Difference between Multiplex and Singleplex PCR Products and Their Practical Implications

BioTechniques ◽  
2000 ◽  
Vol 29 (2) ◽  
pp. 298-308 ◽  
Author(s):  
H.-W. Deng ◽  
Y. Zhou ◽  
R.R. Recker ◽  
M.L. Johnson ◽  
J. Li
Keyword(s):  
Fragment Size ◽  
Size Difference ◽  
Pcr Products ◽  
Practical Implications

Alignment, Scaling, and Size Effects in Discrimination of Graphical Elements

1992 ◽  
Vol 36 (18) ◽  
pp. 1393-1397 ◽  
Author(s):  
J. G. Hollands
Keyword(s):  
Recent Work ◽  
Size Effects ◽  
Response Times ◽  
Size Difference ◽  
Graphical Display ◽  
Percent Difference ◽  
Mental Operations ◽  
Graphical Design ◽  
Practical Implications ◽  
Graphical Perception

Recent work in graphical perception has attempted to identify the mental operations used by an observer when extracting information from a graphical display (e.g., Hollands and Spence, in press; Simkin and Hastie, 1987). The current research varied the alignment, scaling, and size of proportions shown in pie charts and divided bar graphs. Subjects were required to discriminate between two proportions (i.e., which proportion is larger?), each shown relative to its own whole. Response times and errors were measured. Results from Experiment 1 show that for both pies and divided bars, the time penalty for discriminating unaligned proportions was dependent on the size difference between the two proportions, with a greater penalty with a smaller percent difference. Results from Experiment 2 show that different scaling slowed subjects considerably, especially when the size difference was small, and especially with divided bars. The results are interpreted in terms of hypothesized alignment, scaling, and discrimination operations. The practical implications for graphical design are also discussed.

Detection of seven polymorphisms associated with colorectal cancer therapeutic response and toxicity

2006 ◽  
Vol 24 (18_suppl) ◽  
pp. 13160-13160
Author(s):  
K. Z. Qu ◽  
Y. Ren ◽  
J. Liu ◽  
A. Sferrozza ◽  
R. A. Bender
Keyword(s):  
Colorectal Cancer ◽  
Data Analysis ◽  
Drug Response ◽  
Fragment Size ◽  
Fluorescent Detection ◽  
First Line Therapy ◽  
Pcr Products ◽  
Wide Variability ◽  
Development And Validation ◽  
Fluorescent Tag

13160 Background: First-line therapy for metastatic colorectal cancer (CRC) is 5-fluorouracil/leucovorin in combination with oxaliplatin (ie, FOLFOX™) or irinotecan (ie, FOLFIRI). Optimizing this therapy for an individual patient, however, is complicated due to wide variability in drug response and potential for toxicity. Such variability may be due to functional genomic polymorphisms in the drug target gene or in the metabolizing or DNA repair enzyme genes. We report, herein, development and validation of 2 new assays that, together, detect 7 polymorphisms associated with CRC drug response and toxicity. Methods: The first assay (SNaPshot) simultaneously detects 4 polymorphisms by using primers targeting the ERCC1, XPD, GST-P1, and XRCC-1 genes, single nucleotide primer extension of PCR products, electrophoresis and fluorescent detection on an ABI PRISM® 3100 Genetic Analyzer, and data analysis using GeneMapper® software (Applied Biosystems, Inc.). The second assay (F-PCR) simultaneously detects 3 polymorphisms using paired primers targeting the TS and UGT1A1 genes. One primer per pair is labeled with a fluorescent tag, and electrophoresis, detection, and data analysis are performed as described for the SNaPshot assay. Results: Based on fragment size and color, the intra- and interassay precision for SnaPshot ranged from 0.04%-0.51% and 0.14%-0.59%, respectively, and for F-PCR from 0.02%-0.16% and 0.09%-0.29%, respectively. There was 100% concordance in the genotypes determined in 3 separate SNaPshot (n=44 samples) and F-PCR (n=32 samples) assays. Furthermore, there was 100% agreement between genotypes determined by the SNaPshot method and those determined by RFLP (n=10) and between genotypes determined by the F-PCR method and those determined by pyrosequencing (n=17). Conclusions: Our multiplex SNaPshot and F-PCR methods can accurately detect 7 polymorphisms associated with CRC drug response and toxicity. These multiplex PCRs should lead to improved precision and ease of interpretation relative to that of single PCR methods. These methods may help the clinician optimize CRC therapy for individual patients. No significant financial relationships to disclose.

scholarly journals Molecular Analysis of Vitex Species Using Candidate DNA Barcoding and PCR-RFLP of the matK Gene for Authentication of Vitex glabrata

2013 ◽  
Vol 8 (1) ◽  
pp. 1934578X1300800 ◽  
Author(s):  
Waranyoo Phoolcharoen ◽  
Suchada Sukrong
Keyword(s):  
Folk Medicine ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Size Difference ◽  
Dna Barcodes ◽  
Pcr Rflp ◽  
Matk Gene ◽  
Pcr Products ◽  
The Difference ◽  
Vitex Species

Several species of the Vitex genus, family Lamiaceae, are used in folk medicine for a variety of remedies. V. glabrata is unique among Vitex species because its main effect is sexual enhancement. However, crude drugs derived from different Vitex species might not be easily distinguishable, which could lead to their misidentification and misuse. Therefore, the accurate authentication of V. glabrata is critical for its effective medicinal use. In this study, the mat K gene and the psbA- trnH intergenic spacer candidate DNA barcodes were sequenced and analyzed to identify five different Vitex species that are medicinally used in Thailand: V. negundo, V. trifolia, V. rotundifolia, V. limonifolia, and V. glabrata. Each region was successfully amplified from the leaves of the five species using a single set of primers, and the sequences determined. The size difference in PCR products of psb A- trn H and PCR restriction fragment length polymorphism (PCR-RFLP) of the matK gene sequences were used to differentiate V. glabrata from other Vitex species. These results indicate both the matK gene and the psbA-trnH intergenic spacer as candidate DNA barcodes of Vitex species and suggest that the difference of psbA-trnH PCR products and PCR-RFLP analysis based on the mat K gene are effective for the authentication of V. glabrata.

scholarly journals Identification and phylogeny of some species of the genera Sporidiobolus and Rhodotorula using analysis of the 5.8s rDNA gene and two ribosomal internal transcribed spacers

2011 ◽  
Vol 63 (1) ◽  
pp. 79-88 ◽  
Author(s):  
M. Mokhtari ◽  
H.R. Etebarian ◽  
S.H. Mirhendi ◽  
M. Razavi
Keyword(s):  
Yeast Species ◽  
Fragment Size ◽  
Internal Transcribed Spacers ◽  
Rhodotorula Mucilaginosa ◽  
Yeast Identification ◽  
5.8S Rdna ◽  
Electrophoretic Patterns ◽  
Yeast Strains ◽  
Pcr Products ◽  
Its1 And Its2

Due to the problems encountered in routine morphological and physiological procedures that are used in yeast identification, DNA-based methods have recently been developed. In the present study, l66 yeast strains were isolated from several apple and citrus cultivars. After analysis by basic morphological methods, the ITS1 and ITS2 regions of the isolates were amplified separately, and the isolates were grouped based on fragment size polymorphism (FSP) of the amplicons. By comparing the electrophoretic patterns of the PCR products with Rhodotorula mucilaginosa, species were identified as Rhodotorula. For precise and final identification, the ITS-PCR products were subjected to sequencing followed by Blast analysis. As a result, eight isolates were identified as belonging to the Rhodotorula genus, of which five were identified as R. mucilaginosa and three as R. glutinis, and one as a Sporidiobolus. We conclude that the method PCR-FSP, in combination with other approaches, is useful for the identification of yeast species.

scholarly journals Karakteristik Fragmen Gen Penyandi Cytochrome C Oxidase Subunit I (COI) Hama Kepik Penghisap Buah Kakao (Theobroma cacao L.)

bionature ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Muzuni Muzuni
Keyword(s):  
Nucleotide Sequence ◽  
Fragment Size ◽  
Coi Gene ◽  
Restriction Map ◽  
Pcr Product ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Alignment Analysis ◽  
Hydrophobicity Profile ◽  
Theobroma Cacao L

Abstract The purpose of this research is to know the character of partial sequences of the COI gene form fruit-sucking pest. The gene fragments were isolated using PCR (Polymerase Chain Reaction) techniques with specific primers, HlpF and HlpR. Character of gene fragments observed were fragment size, nucleotide sequence, similiarity, restriction map, and hydrophobicity. The size of the fragment was determined by electrophoresis of PCR products, similarity values were determined by aligning the nucleotide sequence of the PCR product with the nucleotides present in GenBank, the restriction map determined by the RestrictionMapper program, and the hydrophobicity profile determined by the BioEdit program. The results showed that PCR yield fragment size 552 pb. The results of alignment analysis showed that PCR fragment had similarity of 88% with Helopeltis theivora, 87% with Helopeltis antonii, 87% with Helopeltis bradyi and 84% with Pacipeltis maesarum. Based on the results of the analysis using RestrictionMapper program shows partial sequences of the COI gene form fruit-sucking pest has 25 sites of restriction enzyme cutting which is class of type II endonuclease enzyme. The results of the hydrophobicity analysis using the BioEdit program indicate that the COI protein is hydrophilic and hydrophobic which shows the integrated COI protein on the membrane.Keywords: COI gene fragment, fruit-sucking pest, PCR, Cocoa Crop

The Differential Effectiveness of the Cognitive Interview Instructions for Enhancing Witnesses’ Memory of a Familiar Event

2014 ◽  
Vol 73 (1) ◽  
pp. 25-34 ◽  
Author(s):  
Magali Ginet ◽  
Jacques Py ◽  
Cindy Colomb
Keyword(s):  
Cognitive Interview ◽  
Critical Event ◽  
Surgical Operation ◽  
Differential Effectiveness ◽  
Correct Information ◽  
Control Instruction ◽  
The Individual ◽  
Practical Implications

This study examines the influence of familiarity on witnesses’ memory and the individual effectiveness of each of the four cognitive interview instructions in improving witnesses’ recall of scripted events. Participants (N = 195), either familiar or unfamiliar with the hospital script, were presented with a video of a surgical operation. One week later, an interviewer used one of the four cognitive interview instructions or a control instruction to ask them about the video. Participants familiar with the surgery context recalled significantly more correct information and, in particular, more consistent and irrelevant details than those unfamiliar with the surgery context. Furthermore, the results confirmed the effectiveness of all four cognitive interview mnemonics in enhancing the amount of correct information reported, irrespective of the participants’ familiarity with the critical event. However, their efficacy differed depending on the category of details considered. The practical implications of these results are discussed.

How Do People Share Their Positive Events?

2016 ◽  
Vol 37 (4) ◽  
pp. 250-259 ◽  
Author(s):  
Cara A. Palmer ◽  
Meagan A. Ramsey ◽  
Jennifer N. Morey ◽  
Amy L. Gentzler
Keyword(s):  
Cluster Analysis ◽  
Communication Technology ◽  
Big Five ◽  
Well Being ◽  
Big Five Personality Traits ◽  
Big Five Personality ◽  
Positive Events ◽  
Growing Body ◽  
Sharing Patterns ◽  
Practical Implications

Abstract. Research suggests that sharing positive events with others is beneficial for well-being, yet little is known about how positive events are shared with others and who is most likely to share their positive events. The current study expanded on previous research by investigating how positive events are shared and individual differences in how people share these events. Participants (N = 251) reported on their likelihood to share positive events in three ways: capitalizing (sharing with close others), bragging (sharing with someone who may become jealous or upset), and mass-sharing (sharing with many people at once using communication technology) across a range of positive scenarios. Using cluster analysis, five meaningful profiles of sharing patterns emerged. These profiles were associated with gender, Big Five personality traits, narcissism, and empathy. Individuals who tended to brag when they shared their positive events were more likely to be men, reported less agreeableness, less conscientiousness, and less empathy, whereas those who tended to brag and mass-share reported the highest levels of narcissism. These results have important theoretical and practical implications for the growing body of research on sharing positive events.

Cross-Lagged Relationships Between Self-Esteem, Self-Construal, and Happiness in a Three-Wave Longitudinal Study

2019 ◽  
Vol 40 (3) ◽  
pp. 177-185
Author(s):  
Daniela Moza ◽  
Laurențiu Maricuțoiu ◽  
Alin Gavreliuc
Keyword(s):  
Structural Equation ◽  
Time Lag ◽  
Self Esteem ◽  
Equation Modeling ◽  
Future Research ◽  
Cross Sectional ◽  
Self Construal ◽  
Self Worth ◽  
Practical Implications ◽  
Independent Person

Abstract. Previous research established that an independent construal of the self is associated with higher self-esteem, which, in turn, is associated with increased happiness. Regarding the directionality of these relationships, theoretical arguments have suggested that self-construal precedes self-esteem and that self-esteem precedes happiness. However, most research in this area is cross-sectional, thus limiting any conclusions about directionality. The present study tested these relationships in 101 Romanian undergraduates using a 3-wave cross-lagged design with a 6-month time lag between every two waves. Structural equation modeling analyses revealed that self-esteem is an antecedent of both happiness and dimensions of independent self-construal (i.e., consistency vs. variability and self-expression vs. harmony). In other words, one’s positive evaluation of self-worth precedes one’s self-perception as being a happy and independent person. The findings are discussed with respect to the theoretical and practical implications, along with limitations and suggestions for future research.

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