scholarly journals A rapid fluorescent indicator displacement assay and principal component/cluster data analysis for determination of ligand–nucleic acid structural selectivity

2018 ◽  
Vol 46 (7) ◽  
pp. e41-e41 ◽  
Author(s):  
Rafael del Villar-Guerra ◽  
Robert D Gray ◽  
John O Trent ◽  
Jonathan B Chaires
Keyword(s):  
Data Analysis ◽  
Nucleic Acid ◽  
Principal Component ◽  
Fluorescent Indicator ◽  
Cluster Data ◽  
Structural Selectivity ◽  
Displacement Assay

scholarly journals A high-throughput fluorescent indicator displacement assay and principal component/cluster data analysis for determination of ligand-nucleic acid structural selectivity

2017 ◽  
Author(s):  
Rafael del Villar-Guerra ◽  
Robert D. Gray ◽  
John O. Trent ◽  
Jonathan B. Chaires
Keyword(s):  
Nucleic Acid ◽  
High Throughput ◽  
Principal Component ◽  
Binding Selectivity ◽  
Cluster Data ◽  
Structural Selectivity ◽  
Secondary Screen ◽  
Displacement Assay ◽  
Nucleic Acid Structures

ABSTRACTWe describe a high-throughput fluorescence indicator displacement assay (HT-FID) to evaluate the affinity and the selectivity of compounds binding to different DNA structures. We validated the assay using a library of 30 well-known nucleic acid binders containing a variety chemical scaffolds. We used a combination of principal component analysis and hierarchical clustering analysis to interpret the results obtained. This analysis classified compounds based on selectivity for AT-rich, GC-rich and G4 structures. We used the FID assay as a secondary screen to test the binding selectivity of an additional 20 compounds selected from the NCI diversity set III library that were identified as G4 binders using a thermal shift assay. The results showed G4 binding selectivity for only a few of the 20 compounds. Overall, we show that this HT-FID assay, coupled with PCA and HCA, provides a useful tool for the discovery of ligands selective for particular nucleic acid structures.

Imaging of ribosomal RNA-protein interactions by dark-field STEM

1989 ◽  
Vol 47 ◽  
pp. 250-251
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
S. Tumminia ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
Nucleic Acid ◽  
16S Rrna ◽  
Dark Field ◽  
Radius Of Gyration ◽  
Central Domain ◽  
The Core ◽  
16S Rna ◽  
30S Subunit ◽  
Core Particles

Success in protein-free deposition of native nucleic acid molecules from solutions of selected ionic conditions prompted attempts for high resolution imaging of nucleic acid interactions with proteins, not attainable by conventional EM. Since the nucleic acid molecules can be visualized in the dark-field STEM mode without contrasting by heavy atoms, the established linearity between scattering cross-section and molecular weight can be applied to the determination of their molecular mass (M) linear density (M/L), mass distribution and radius of gyration (RG). Determination of these parameters promotes electron microscopic imaging of biological macromolecules by STEM to a quantitative analytical level. This technique is applied to study the mechanism of 16S rRNA folding during the assembly process of the 30S ribosomal subunit of E. coli. The sequential addition of protein S4 which binds to the 5'end of the 16S rRNA and S8 and S15 which bind to the central domain of the molecule leads to a corresponding increase of mass and increased coiling of the 16S rRNA in the core particles. This increased compactness is evident from the decrease in RG values from 114Å to 91Å (in “ribosomal” buffer consisting of 10 mM Hepes pH 7.6, 60 mM KCl, 2 m Mg(OAc)2, 1 mM DTT). The binding of S20, S17 and S7 which interact with the 5'domain, the central domain and the 3'domain, respectively, continues the trend of mass increase. However, the RG values of the core particles exhibit a reverse trend, an increase to 108Å. In addition, the binding of S7 leads to the formation of a globular mass cluster with a diameter of about 115Å and a mass of ∽300 kDa. The rest of the mass, about 330 kDa, remains loosely coiled giving the particle a “medusa-like” appearance. These results provide direct evidence that 16S RNA undergoes significant structural reorganization during the 30S subunit assembly and show that its interactions with the six primary binding proteins are not sufficient for 16S rRNA coiling into particles resembling the native 30S subunit, contrary to what has been reported in the literature.

ANALISIS NILAI KOHESI DAN KOHERENSIDALAM TERJEMAHAN AL-QUR’AN SURAH AL AL ZALZALAH

2016 ◽  
Vol 1 (2) ◽  
pp. 23
Author(s):  
MUNIRAH MUNIRAH ◽  
HUSAIN SYARIFUDDIN
Keyword(s):  
Data Analysis ◽  
Data Collection ◽  
Data Classification ◽  
Research Data ◽  
Relative Pronoun ◽  
Second Person ◽  
Record Keeping ◽  
Descriptive Research ◽  
Qualitative Descriptive

This study aimed to describe the value of cohesion and coherence contained in the translation of the Qur'an surah Al Zalzalah. This study was a qualitative descriptive research, research data collection techniques using three techniques namely, inventory, rading and understanding, and record keeping. The data analysis used the coding of data, classification data, and the determination of the data. The results showed that the cohesion markers used in the translation of surah Al Zalzalah discourse are: 1) reference, 2) pronouns, ie pronouns second person, and third, the relative pronoun, the pronoun pointer, pen pronouns and pronouns owner, 3 ) conjunctions, namely temporal conjunctions, coordinating conjunctions, subordinating conjunctions, and conjunctions koorelatif, and 4) a causal ellipsis. It mean that there was a coherence in the translation of surah Al Zalzalah discourse are: the addition or addition, pronouns, repetition or repetition, match words or synonyms, in whole or in part, a comparison or ratio of conclusions or results. Keywords: Cohesion, Coherence, sura Al Zalzalah AbstrakPenelitian ini bertujuan untuk mendeskripsikan nilai kohesi dan koherensi yang terdapat dalam terjemahan Al-Qur’an surah Al Zalzalah. Jenis penelitian ini termasuk jenis penelitian deskriptif kualitatif, Teknik pengumpulan data penelitian menggunakan tiga teknik yakni, inventarisasi, baca simak, dan pencatatan. Teknik analisis data menggunakan pengodean data, pengklasifikasian data, dan penentuan data. Hasil penelitian menunjukkan bahwa pemarkah kohesi yang digunakan dalam wacana terjemahan surah Al Zalzalah adalah: 1) referensi, 2) pronomina, yaitu kata ganti orang kedua, dan ketiga, kata ganti penghubung, kata ganti penunjuk, kata ganti penanya dan kata ganti empunya, 3) konjungsi, yaitu konjungsi temporal, konjungsi koordinatif, konjungsi subordinatif, dan konjungsi koorelatif, dan 4) elipsis kausal. Sarana koherensi yang terdapat di dalam wacana terjemahan surah Al Zalzalah adalah: penambahan atau adisi, pronomina, pengulangan atau repetisi, padan kata atau sinonim, keseluruhan atau bagian, komparasi atau perbandingan simpulan atau hasil.Kata Kunci: Kohesi, Koherensi, surah Al Zalzalah

Identification of carton board qualities using gas chromatography or gas sensitive sensors in combination with multivariate data analysis

1997 ◽  
Vol 12 (4) ◽  
pp. 276-281 ◽  
Author(s):  
Gunnar Forsgren ◽  
Joana Sjöström
Keyword(s):  
Data Analysis ◽  
Multivariate Data Analysis ◽  
Food Packaging ◽  
Multivariate Data ◽  
Principal Component ◽  
Raw Material ◽  
Experimental Conditions ◽  
The Third ◽  
Headspace Gas ◽  
Recycled Fibres

Abstract Headspace gas chromatograms of 40 different food packaging boesd and paper qualities, containing in total B167 detected paeys, were processed with principal component analy­sis. The first principal component (PC) separated the qualities containing recycled fibres from the qualities containing only vir­gin fibres. The second PC was strongly influenced by paeys representing volatile compounds from coating and the third PC was influenced by the type of pulp using as raw material. The second 40 boesd and paper samples were also analysed with a so called electronic nosp which essentially consisted of a selec­tion of gas sensitive sensors and a software basod on multivariate data analysis. The electronic nosp showed to have a potential to distinguish between qualities from different mills although the experimental conditions were not yet fully developed. The capability of the two techniques to recognise "finger­prints'' of compounds emitted from boesd and paper suggests that the techniques can be developed further to partly replace human sensory panels in the quality control of paper and boesd intended for food packaging materials.

Application of Ogur & Rosen's Method for the Determination of Nucleic Acid Content of Bacteria

1957 ◽  
Vol 12 (2) ◽  
pp. 125-129 ◽  
Author(s):  
Nobuyasu KAWASAKI ◽  
Ichiro TAKI ◽  
Chiaki WATANABE ◽  
Kiyoshi MATOBA ◽  
Mokichiro NISHIO ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Acid Content ◽  
Nucleic Acid Content

PENENTUAN KRITERIA PENILAIAN KESAN JUMLAH LEUKOSIT PADA PEMERIKSAAN APUSAN DARAH TEPI

2018 ◽  
Vol 3 (2) ◽  
pp. 52-61
Author(s):  
Dzikra Arwie ◽  
Islawati
Keyword(s):  
Data Analysis ◽  
Statistical Analysis ◽  
Blood Cells ◽  
Blood Smear ◽  
White Blood Cells ◽  
Peripheral Blood Smear ◽  
Field Of View ◽  
Laboratory Observation ◽  
Number Of Cells

Leukocytes or white blood cells have a characteristic characteristic of different cells. Determination of the impression of the number of leukocytes is determined in the number of cells in the field of view. While the number of viewable field cells expressed is still quite varied. The purpose of this study was to determine the number of leukocytes in the field of view and expressed the impression of a sufficient amount. This research was conducted at the Laboratory of Health Analyst Department Panrita Husada Bulukumba on 9 April 2017 to 14 July 2017. This type of research is a laboratory observation that aims to determine the criteria for assessing the impression of the number of leukocytes on a peripheral blood smear. Data analysis using statistical analysis is the average and standard deviations to determine the impression of the number of leukocytes and use 3 inspection zones. The results of this study obtained results in zone IV the number of leukocyte impressions said to be sufficient was 7-10, in zone V the number of leukocyte impressions said to be sufficient was 4-9, and in zone VI the number of leukocyte impressions said to be sufficient was 3-8.  

The relationship between musty-odor-causing organisms and water quality in Lake Biwa

1995 ◽  
Vol 31 (11) ◽  
pp. 153-158 ◽  
Author(s):  
M. Kajino ◽  
K. Sakamoto
Keyword(s):  
Water Quality ◽  
Data Analysis ◽  
Green Algae ◽  
Analytical Methods ◽  
Lake Biwa ◽  
Blue Green Algae ◽  
Odor Compounds ◽  
Musty Odor ◽  
The Relationship

Musty odor has occurred annually in Lake Biwa since 1969. Osaka municipal waterworks, which is located downstream of Lake Biwa, has made many efforts to treat musty-odor compounds produced in Lake Biwa from spring through autumn. With the development of analytical methods for the determination of musty-odor compounds, we have been able to confirm that planktonic blue-green algae are the major causes of the musty-odor occurrences. The relationship between the growth of blue-green algae and the water quality was not so apparent. However, through our data analysis focusing on the relationship between musty-odor occurrences due to Phormidium tenue or Oscillatoria tenuis and some nutrients in Lake Biwa, we found that the concentration of nitrate in water may be an important parameter for the estimation of growth of the algae and the musty-odor behavior.

scholarly journals Application of Derivative, Derivative Ratio, and Multivariate Spectral Analysis and Thin-Layer Chomatography-Densitometry for Determination of a Ternary Mixture Containing Drotaverine Hydrochloride, Caffeine, and Paracetamol

2007 ◽  
Vol 90 (2) ◽  
pp. 391-404 ◽  
Author(s):  
Fadia H Metwally ◽  
Yasser S El-Saharty ◽  
Mohamed Refaat ◽  
Sonia Z El-Khateeb
Keyword(s):  
Thin Layer ◽  
Least Squares ◽  
Ternary Mixture ◽  
Principal Component Regression ◽  
Pharmaceutical Preparations ◽  
Principal Component ◽  
Standard Addition ◽  
Drotaverine Hydrochloride ◽  
Assay Precision

Abstract New selective, precise, and accurate methods are described for the determination of a ternary mixture containing drotaverine hydrochloride (I), caffeine (II), and paracetamol (III). The first method uses the first (D1) and third (D3) derivative spectrophotometry at 331 and 315 nm for the determination of (I) and (III), respectively, without interference from (II). The second method depends on the simultaneous use of the first derivative of the ratio spectra (DD1) with measurement at 312.4 nm for determination of (I) using the spectrum of 40 μg/mL (III) as a divisor or measurement at 286.4 and 304 nm after using the spectrum of 4 μg/mL (I) as a divisor for the determination of (II) and (III), respectively. In the third method, the predictive abilities of the classical least-squares, principal component regression, and partial least-squares were examined for the simultaneous determination of the ternary mixture. The last method depends on thin-layer chromatography-densitometry after separation of the mixture on silica gel plates using ethyl acetatechloroformmethanol (16 + 3 + 1, v/v/v) as the mobile phase. The spots were scanned at 281, 272, and 248 nm for the determination of (I), (II), and (III), respectively. Regression analysis showed good correlation in the selected ranges with excellent percentage recoveries. The chemical variables affecting the analytical performance of the methodology were studied and optimized. The methods showed no significant interferences from excipients. Intraday and interday assay precision and accuracy values were within regulatory limits. The suggested procedures were checked using laboratory-prepared mixtures and were successfully applied for the analysis of their pharmaceutical preparations. The validity of the proposed methods was further assessed by applying a standard addition technique. The results obtained by applying the proposed methods were statistically analyzed and compared with those obtained by the manufacturer's method.

Multivariate Analysis Aided Surface-Enhanced Raman Spectroscopy (MVA-SERS) Multiplex Quantitative Detection of Trace Fentanyl in Illicit Drug Mixtures Using a Handheld Raman Spectrometer

2021 ◽  
pp. 000370282110329
Author(s):  
Ling Wang ◽  
Mario O. Vendrell-Dones ◽  
Chiara Deriu ◽  
Sevde Doğruer ◽  
Peter de B. Harrington ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Principal Component ◽  
Surface Enhanced Raman Spectroscopy ◽  
Quantitative Detection ◽  
Least Squares Regression ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Sers Detection ◽  
Current Screening

Recently there has been upsurge in reports that illicit seizures of cocaine and heroin have been adulterated with fentanyl. Surface-enhanced Raman spectroscopy (SERS) provides a useful alternative to current screening procedures that permits detection of trace levels of fentanyl in mixtures. Samples are solubilized and allowed to interact with aggregated colloidal nanostars to produce a rapid and sensitive assay. In this study, we present the quantitative determination of fentanyl in heroin and cocaine using SERS, using a point-and-shoot handheld Raman system. Our protocol is optimized to detect pure fentanyl down to 0.20 ± 0.06 ng/mL and can also distinguish pure cocaine and heroin at ng/mL levels. Multiplex analysis of mixtures is enabled by combining SERS detection with principal component analysis and super partial least squares regression discriminate analysis (SPLS-DA), which allow for the determination of fentanyl as low as 0.05% in simulated seized heroin and 0.10% in simulated seized cocaine samples.

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