Cyanines are resonant dyes characterized by polymethine dyes between nitrogen atoms (two atoms of nitrogen) with a delocalized charge. Because of low non-specific binding to biomolecules as well as bright fluorescence, cyanines have become some of the most popular fluorescent dyes for labeling nucleic acids.

Fluorescein and rhodamine dyes are the ones most commonly used to develop biological sensing probes.

Fluorescent dyes, also known as reactive dyes or fluorophores, have been used by biologists for decades. Fluorescent dyes offer higher photostability and brightness compared to fluorescent proteins and do not require a maturation time.

a stain or staining procedure using a fluorescent dye or substance that will combine selectively with certain tissue components and that will then fluoresce upon irradiation with ultraviolet or violet-blue light.

The use of fluorescent stains to visually investigate eukaryotic and/or prokaryotic cells is increasing quickly and manuscripts within all areas of research publish results using fluorescent staining techniques.

Haematoxylin and eosin (H&E) staining Haematoxylin and eosin staining is frequently used in histology to examine thin tissue sections. Haematoxylin stains cell nuclei blue, while eosin stains cytoplasm, connective tissue and other extracellular substances pink or red.

It stains basic (or acidophilic) structures red or pink. This is also sometimes termed ‘eosinophilic’. Thus the cytoplasm is stained pink in the picture below, by H&E staining. Haematoxylin can be considered as a basic dye (general formula for basic dyes is:dye+ Cl-).

The Schaeffer-Fulton method (the most commonly used endospore-staining technique) uses heat to push the primary stain (malachite green) into the endospore. Washing with water decolorizes the cell, but the endospore retains the green stain. The cell is then counterstained pink with safranin.

There are three broad categories of biological stains:

• General or Routine Stains: Used to differentiate between the nucleus and the cytoplasm.
• Special Stains: These are used to demonstrate specific elements within the tissue, such as connective tissue, muscle, carbohydrates, lipids, pigments, and nerve tissue.

SIMPLE STAIN: It is a cationic dye (positive charge) which stains the cell a blue color. The presence of negatively charged molecules in the cell (like DNA & RNA) causes the cell to stain blue.

Microscopic examination of clinical samples for acid-fast bacilli using the Ziehl-Neelsen (ZN) stain has been a standard diagnostic tool and is used globally for rapid TB diagnosis. Microscopy can detect 60% to 70% of culture-positive samples with a lower limit of detection of 5 × 103 organisms/mL.

True to its name, the simple stain is a very simple staining procedure involving a single solution of stain. Any basic dye such as methylene blue, safranin, or crystal violet can be used to color the bacterial cells.

In a simple staining technique, a positively charged stain colors the negatively charged cells, making them stand out against the light background. In a negative staining technique, a negatively charged stain colors the background, leaving the cells light colored and unstained.

Some suitable negative stains include ammonium molybdate, uranyl acetate, uranyl formate, phosphotungstic acid, osmium tetroxide, osmium ferricyanide and auroglucothionate. The structures which can be negatively stained are much smaller than those studied with the light microscope.

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Principle of Negative Staining Negative staining requires an acidic dye such as India Ink or Nigrosin. India Ink or Nigrosin is an acidic stain. This means that the stain readily gives up a hydrogen ion (proton) and the chromophore of the dye becomes negatively charged.

It is used when looking at capsules and yeast or spirochetes that do not stain well. Negative stain is used when viewing bacteria by wet mount or hanging drop slide to view bacterial motility.