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Agar gelation is the primary application of agar and agarose and there a number of factors that disturb it, here we will try to cover them. To elevate the agar gel strength, in 1946, Yanagawa alkali treated the agar to convert L-galactose 6-sulfate into 3,6-anhydrogalactose and Rees used sulfate alkyl-transferase in algae and succeeded. This chemical reaction affects the rheological characteristics of agar and can be understand with respect to the so-called gel network theory coined and studied during the period of 1969–1982 [23–27].

Factors that affect the physico-chemical properties of algae, also affect the synthesis of agar as well as its yield. A number of authors have studied the seasonal quality of agar and published the researched data.

Multiple fractionation patterns, using anion-exchange chromatography, were discovered by Ji et al. in 1985. He observed multiple 6-O-methyl-D-galactose fractions in Gracilaria verrucosa agar of North and South China. The differences in patterns must be due to the different origin sites of agar, still genetic dissimilarity could not be taken away. Rees and Conway studied correlation of 3,6-anhydro-galactose fractions in Porphyra agars with environmental conditions.

After all these studies, it can be stated that it is not easy to assess the effect of seasons or the effect of any biological factor or location effect upon the quality of agar. The reason behind this is the different types of extraction and purification processes that are involved. Moreover, there can be a number of factors, that are unknown, and varies from site to site and species to species of algae. To evaluate the effect of definite constraint, a synthesized agar using defined parameters of purification and extraction process, can be used. From 1981 to 1989, Chiles et al. [28], Craige et al. and Charles et al. studied the agar of some Gracilaria species by altering their nitrogen contents. If the nitrogen content of the culture medium is increased and later alkali treated, it increases the thallus nitrogen content, which gives less agar yield but higher gel strength. Conversely in 1989 Chiles doubted the fact that higher agar yield can be achieved in lower nitrogen conditions, because these extracted agars have higher starch contents than the regular ones. Because this starch contamination cannot be totally removed using regular purification techniques thus may result in interference in the mechanical properties of agar gel. This starch contamination can be removed by using heat stable amylases like Termamyl or amyloglucosidase during the extraction process of agar. Nitrogen content of culture medium acted as the limiting growth factor of the algae. By changing the temperature of water and changing the light and/or biomass density, of Gracilaria cultures, its growth rate can be limited. These factors are supposed to affect the population of agar and its chemistry. For example; agar of low gel strength from G. tikvahiae was obtained by elevating the water temperature to 27 °C. It also changed 3,6-anhydrogalactose content and increased the concentration of 4-O-methyl-L-galactose and sulfates in this alkali altered agar.

In G. tikvahiae, the quality of the agar is inversely related with its age. According to Craigie and Wen, younger tissues of agar have higher content of 3,6-anhydrogalactose, however old tissues have more methyl and sulfate contents in them. The young and old tissues of Gracilaria pseudoverrucosa during growing and non-growing seasons with respect to the changes in chemical structure and agar distribution throughout the algae, was studied by Lahaye and Yaphe in 1988. They stated that chemical structure of agar changes with the algal age, and called it “secondarization” of algal cell-wall. Precursor-repeating units are higher in the polysaccharides of younger or ‘primary’ cell wall of algae. This affects the physico-chemical properties of agar gel i.e.: enrichment of precursor-repeating units leads to decrease in limitation in elongation of dividing cell and actively growing tissues. However, when algal tissue gets old, fewer cell division occurs and cell wall thickens and gets flexible to stabilize the algal skeleton. When agar polysaccharide is synthesized and/or substituted with chemical groups, or make cross-links with it, it increases the rigidity and cohesiveness of the older cell wall or ‘secondarized’ cell wall. The more rigid cell wall provides the protection to algae towards the pathogens as well as increases its resistance.

Kim and Henriquez in 1978 and Whyte in 1981 [29], proposed the life history of an alga, affect the quality of agars. It was observed that cystoscarpic G. verrucosa yielded a higher amount of agar with poor quality, compared to the other tetrasporic plants. The agar quality, particularly in G. verrucosa, is decreased in following order; cystoscarpic, tetrasporic, vegetative and male gametophyte. Young immature vegetative growth of G. verrucosa has ‘incomplete’ agar, supplemented with L-galactose 6-sulfate. But no major differences were found in the agar produced by male or female gametophytes, or any tetrasporophytic G. verrucosa. In the same way no major differences were found in the agar quality, obtained from various developmental stages of agarophyte Gracilaria bursa-postoris, Gracilaria coronopifolia, G. verrucosa and Onikusa pristoides. However in carrageenophyte, the quality of the agar gel and its structure doesn’t get affected by the different stages of algal life.

As a consequence, it will be good to use ‘agar’ as a standard term for the repetitive interrelated molecules based on repeated units of agarobiose. These types of polysaccharides differ in their physico-chemical and chemical properties all through their algal genotypes and even within the algal species. Since this polysaccharide family is so diverse in such a way that the nature of agar gel gets affected by physiological, cellular as well as by environmental factors. Thus not only physico-chemical but also chemical alterations due to these factors, should be explicated.