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Related Concept Videos

Standard Deviation01:10

Standard Deviation

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The most commonly used measure of variation is the standard deviation. It is a numerical value measuring how far data values are from their mean. The standard deviation value is small when the data are concentrated close to the mean, exhibiting slight variation or spread. The standard deviation value is never negative, it is either positive or zero. The standard deviation is larger when the data values are more spread out from the mean, which means the data values are exhibiting more variation.
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Mean Absolute Deviation01:13

Mean Absolute Deviation

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The mean absolute deviation is also a measure of the variability of data in a sample. It is the absolute value of the average difference between the data values and the mean.
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Variation: Normal Distribution, Range, and Standard Deviation02:32

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In the field of psychology, there are several ways to organize measurements of a trait, feature, or characteristic (i.e., variables). Qualitative data, such as ethnicity, can be tabulated into a frequency count to provide information about the proportion, as well as the variety of groups in a sample or population. On the other hand, researchers can perform a wider set of calculations on quantitative data. The mean, mode, and median, for instance, are central tendency measures to identify a...
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Wnt is a zygotic effect gene that is expressed during very early embryonic development. It regulates various processes in animals starting from early development through the adult stage, such as organogenesis in the embryo and maintenance of neuronal and blood stem cells. Wnt proteins can induce a wide variety of intracellular pathways depending upon the specific abilities of different Wnt ligands to form a complex with shared and cognate receptors in the presence of different co-receptors. The...
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Standard Deviation of Calculated Results01:14

Standard Deviation of Calculated Results

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Standard deviation measures the spread of data around the mean value. Many large data sets follow a Gaussian distribution, also known as a normal distribution. This distribution is bell-shaped curved, with the most frequently observed value (mean or central value) in the middle. The farther away from the central value, the greater the deviation from the central value, and the lower the frequency.
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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling
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Sequence-Dependent Deviations of Constrained DNA from Canonical B-Form.

Kfir Kuchuk1, Liat Katrivas2, Alexander Kotlyar2

  • 1Department of Physics and the Russell Berrie Nanotechnology Institute , Technion - Israel Institute of Technology , Haifa 3200003 , Israel.

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High-resolution atomic force microscopy (AFM) reveals that DNA structure in biologically relevant conditions differs from canonical models. This study challenges long-held assumptions about DNA

Keywords:
AFMDNAsingle molecule biophysics

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Area of Science:

  • Biophysics
  • Molecular Biology
  • Structural Biology

Background:

  • Canonical structural models of short DNA exist from crystallographic and NMR studies.
  • In vivo, long DNA molecules face constraints from membranes, proteins, and other molecules, which cannot be tested by existing methods.
  • Previous experimental methods lack the resolution to study DNA structure under biologically relevant constraints.

Purpose of the Study:

  • To investigate the in vivo structure of long DNA molecules under biologically relevant constraints.
  • To compare DNA structures under constrained conditions with canonical models.
  • To highlight the utility of atomic force microscopy (AFM) for single-molecule DNA characterization.

Main Methods:

  • High-resolution frequency-modulation atomic force microscopy (AFM).
  • Imaging of single long DNA molecules: poly(dA)-poly(dT), poly(dG)-poly(dC), and lambda DNA.
  • Utilizing an underlying substrate to emulate biological constraints on DNA structure.

Main Results:

  • Observed systematic, sequence-dependent variations in DNA groove dimensions.
  • Demonstrated that DNA structure under realistic interactions differs from canonical models.
  • Showcased AFM's capability for single-molecule characterization of DNA under constraint.

Conclusions:

  • The structure of DNA in a constrained, biologically relevant environment deviates from established canonical models.
  • Atomic force microscopy (AFM) provides a unique tool for characterizing single DNA molecules under near-physiological conditions.
  • Findings necessitate a re-evaluation of current DNA structural models in the context of cellular environments.