Polymerase Chain Reaction (PCR): Principle and Applications

The characterization of the diversity of species living within ecosystems is of major scientific interest to understand the functioning of these ecosystems. It is also becoming a societal issue since it is necessary to implement the conservation or even the restoration of biodiversity. Historically, species have been described and characterized on the basis of morphological criteria, which are closely linked by environmental conditions or which find their limits especially in groups where they are difficult to access, as is the case for many species of microorganisms. The need to understand the molecular mechanisms in species has made the PCR an indispensable tool for understanding the functioning of these biological systems. A number of markers are now available to detect nuclear DNA polymorphisms. In genetic diversity studies, the most frequently used markers are microsatellites. The study of biological complexity is a new frontier that requires high-throughput molecular technology, high speed computer memory, new approaches to data analysis, and the integration of interdisciplinary skills

The Genetic Diversity Analysis of Tunisian Male Date Palm Cultivars (Phoneix dactylifera L.) Revealed by Phenotypic and Molecular Markers

Tunisian oases reveal an important genetic heritage of date palm cultivars, with various qualities of use. Since the beginning of the century, this heritage has evolved to a selective orientation based on the monoculture of "Deglet Nour," this orientation risks causing the loss of many cultivars. The male of the date palm is part of this heritage and so far remains marginalized. Although they are important for the date palm production cycle, it is in this context that lies our work to study the genetic diversity of a collection of male date palm pollinators from southern Tunisia. The morphological study of the 20 date palm pollinators using 45 IPGRI (International Plant Genetic Resources Institute) descriptors showed significant discrimination, with a similarity index ranging from 0.207 to 0.457, divided them into five similarity groups. The use of 7 ISSR (Inter Simple Sequences Repeat) primers resulted in 64 reproducible bands, of which 57 were 90% polymorphic, and statistical analysis showed a more or less significant genetic diversity with genetic distances 0.491 to 0.873. According to the Mentel test, a non-significant weak correlation (r = 0.015) was noted between the molecular and morphological data. However, the processing of molecular data by various methods generated very significant correlations. Indeed, the correlation between the SM (Simple matching) coefficient and the DICE coefficient showed an important correlation with r = 0.748, which confirms the discriminating power of the ISSR markers in studying the genetic diversity of date palm pollinators

Effect of pollination time, the hour of daytime, pollen storage temperature and duration on pollen viability, germinability, and fruit set of date palm (Phoenix dactylifera L.) cv "Deglet Nour"

Success artificial pollination with viable pollen is crucial process in the production chain of date palms. This study evaluated the impact of pollen storage temperature and duration, pollination time following spathe cracking, and the hour of daytime on pollen viability, germinability, fruit set and yield of 'Deglet Nour' date palm cultivar. In in vitro tests, fresh pollen showed the maximum viability (96.3%) and germination (85%) but it decreased thereafter upon the storage temperature (28, 4 and-30 degrees C) and duration (3, 6, 9 and 12 months). In this respect, pollen stored at-30 degrees C retained highest viability and germinability followed by those stored at 4 and then at 28 degrees C. In filed experiments, fruit set was 85, 75, 65, and 45% with pollination using fresh pollen, or pollen stored at-30, 4 and 28 degrees C, respectively. Fruit set was 95%, 75%, and less than 50%, for pollination performed on the same day of spathe cracking, 6 and 12 days later, respectively. The highest fruit set percentage and yield/bunch were obtained with pollination performed between 12.0 pm and 15.0 pm in contrast to 8.0-11.0 am or 16.0-17.0. (c) 2021 The Author(s). Published by Elsevier B.V. on behalf of King Saud University. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)

Effect of elevated temperature on the hydration heat and mechanical properties of blended cements mortars

This paper presents an experimental investigation for testing the effect of elevated temperature on the hydration heat and mechanical properties of blended cement mortars. Two tests on mortars were made. The first set of mortars is tested of mechanical properties at various temperatures of 20, 35 and 50°C and the second test consists to determine the hydration heat by a semi-adiabatic calorimeter at isothermal temperature of 20, 35 and 50°C during seven days. The new empirical equation has been proposed to estimate the compressive strength depending on the hydration heat for blended cement preserved in constant temperature at early. The results founded from this relationship illustrate a good accuracy with the experimental ones and reflect the best choice to be used to predict the compressive strength depending on the heat of hydration at early age (7 days)

Effect of elevated temperature on the hydration heat and mechanical properties of blended cements mortars

This paper presents an experimental investigation for testing the effect of elevated temperature on the hydration heat and mechanical properties of blended cement mortars. Two tests on mortars were made. The first set of mortars is tested of mechanical properties at various temperatures of 20, 35 and 50°C and the second test consists to determine the hydration heat by a semi-adiabatic calorimeter at isothermal temperature of 20, 35 and 50°C during seven days. The new empirical equation has been proposed to estimate the compressive strength depending on the hydration heat for blended cement preserved in constant temperature at early. The results founded from this relationship illustrate a good accuracy with the experimental ones and reflect the best choice to be used to predict the compressive strength depending on the heat of hydration at early age (7 days)

Parent Concrete Quality of Recycled Concrete Aggregates on Some Engineering Properties of Concrete

This paper aims to investigate some properties of recycled aggregates concrete (RAC) containing various amount of recycled concrete aggregates (RCA) supplied from different parent concrete strength. Three concretes with different strengths were made. After hardening, they were crushed and the obtained RCA were used to substitute 20%, 40% and 60% of coarse ordinary aggregates (COA) in concrete mix. The properties of these RCA according to their parent concrete strength were analyzed and their effects on the workability, compressive strength and shrinkage were quantified. Concrete workability and final shrinkage seem to be related to the equivalent water absorption of coarse recycled aggregates. An equivalent granular expression can be used in classical model to predict compressive strength according to the RCA content and its parent concrete strength.

Parent Concrete Quality of Recycled Concrete Aggregates on Some Engineering Properties of Concrete

This paper aims to investigate some properties of recycled aggregates concrete (RAC) containing various amount of recycled concrete aggregates (RCA) supplied from different parent concrete strength. Three concretes with different strengths were made. After hardening, they were crushed and the obtained RCA were used to substitute 20%, 40% and 60% of coarse ordinary aggregates (COA) in concrete mix. The properties of these RCA according to their parent concrete strength were analyzed and their effects on the workability, compressive strength and shrinkage were quantified. Concrete workability and final shrinkage seem to be related to the equivalent water absorption of coarse recycled aggregates. An equivalent granular expression can be used in classical model to predict compressive strength according to the RCA content and its parent concrete strength.

Stock Prices and Exchange Rates in Indonesia: Further Evidence

The paper examines the relationship between stock prices and exchange rates for the case of Indonesia. The study uses daily and weekly data for the period January 1998 to December 2007. We employed Toda and Yamamoto (1995) Granger non-causality test in both bivariate and multivariate setting to examine the relationship between stock prices and exchange rates. The results of this study suggest a strong evidence of bi-directional causality between these two financial variables. The results have implications for investors, practitioners and policy makers

Benchmarking phasing software with a whole-genome sequenced cattle pedigree.

peer reviewed[en] BACKGROUND: Accurate haplotype reconstruction is required in many applications in quantitative and population genomics. Different phasing methods are available but their accuracy must be evaluated for samples with different properties (population structure, marker density, etc.). We herein took advantage of whole-genome sequence data available for a Holstein cattle pedigree containing 264 individuals, including 98 trios, to evaluate several population-based phasing methods. This data represents a typical example of a livestock population, with low effective population size, high levels of relatedness and long-range linkage disequilibrium. RESULTS: After stringent filtering of our sequence data, we evaluated several population-based phasing programs including one or more versions of AlphaPhase, ShapeIT, Beagle, Eagle and FImpute. To that end we used 98 individuals having both parents sequenced for validation. Their haplotypes reconstructed based on Mendelian segregation rules were considered the gold standard to assess the performance of population-based methods in two scenarios. In the first one, only these 98 individuals were phased, while in the second one, all the 264 sequenced individuals were phased simultaneously, ignoring the pedigree relationships. We assessed phasing accuracy based on switch error counts (SEC) and rates (SER), lengths of correctly phased haplotypes and the probability that there is no phasing error between a pair of SNPs as a function of their distance. For most evaluated metrics or scenarios, the best software was either ShapeIT4.1 or Beagle5.2, both methods resulting in particularly high phasing accuracies. For instance, ShapeIT4.1 achieved a median SEC of 50 per individual and a mean haplotype block length of 24.1 Mb (scenario 2). These statistics are remarkable since the methods were evaluated with a map of 8,400,000 SNPs, and this corresponds to only one switch error every 40,000 phased informative markers. When more relatives were included in the data (scenario 2), FImpute3.0 reconstructed extremely long segments without errors. CONCLUSIONS: We report extremely high phasing accuracies in a typical livestock sample. ShapeIT4.1 and Beagle5.2 proved to be the most accurate, particularly for phasing long segments and in the first scenario. Nevertheless, most tools achieved high accuracy at short distances and would be suitable for applications requiring only local haplotypes

A 660-Kb deletion with antagonistic effects on fertility and milk production segregates at high frequency in Nordic Red cattle : additional evidence for the common occurrence of balancing selection in livestock

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