Management of Evolving Map Data: Data Structures and Algorithms Based on the Framework Map

A consensus framework map of a chromosome is the single most useful map of the chromosome, because of the amount of information it holds as well as the quality of the supporting data backing the putative order of its objects. We describe data structures and algorithms to assist in framework map maintenance and to answer queries about order and distance on genomic objects. We show how these algorithms are efficiently implemented in a client-server relational database. We believe that our data structures are particularly suitable for databases to support collaborative mapping efforts that use heterogeneous methodologies. We summarize two applications that use these algorithms: CHROMINFO, a database specifically designed for framework map maintenance; and the shared client-server database for the chromosome 12 genome center.     

Coimmobilization of D-amino acid oxidase and catalase by entrapment ofTrigonopsis variabilis in radiation polymerised Polyacrylamide beads

Trigonopsis variabilis induced for D-amino acid oxidase and catalase was immobilized by entrapment in Polyacrylamide beads obtained by radiation polymerisation. Permeabilization of the cells was found to be essential for optimal activity of the enzymes in free cells. However, the process of entrapment itself was found to eliminate the permeability barrier of cells immobilized in Polyacrylamide. The two enzymes exhibited a differential response on Polyacrylamide entrapment. Thus, D-amino acid oxidase activity was stabilized to heat inactivation whereas catalase in the same cells showed a destabilization on entrapment in Polyacrylamide. The coimmobilized enzyme preparation showed an operational half life of 7–9 days after which the D-amino acid oxidase activity remained stable at a value 35–40% of that of the initial activity for a study period of 3 weeks. Coimmobilization of MnO₂ was not effective in enhancing the operational life of the enzyme preparation.     

A rapid method for the purification of D-amino acid oxidase of Trigonopsis variabilis by hydrophobic chromatography

Summary A relatively simple method has been described for the rapid purification of D-amino acid oxidase from Trigonopsis variabilis by hydrophobic chromatography on Phenyl-Sepharose CL-4B and negative adsorption on DEAE-cellulose. The purified enzyme had a specific activity of 22–24 units at 25°C and exhibited three bands on enzymatic staining.     

Possible implications of reciprocity between ethylene and aflatoxin biogenesis in Aspergillus flavus and Aspergillus parasiticus.

Aspergillus flavus and Aspergillus parasiticus produced ethylene during early growth. However, the onset of toxin biosynthesis was marked by the absence of ethylene evolution. 2-Chloroethyl phosphonic acid, an ethylene-generating compound, inhibited aflatoxin biosynthesis in vivo. The reciprocal relationship between the production of aflatoxin and ethylene by the organism may indicate the involvement of the latter in the regulation of aflatoxin biogenesis.     

Hydrolysis of milk lactose by immobilized beta-galactosidase-hen egg white powder

Immobilized beta-galactosidase was obtained by crosslinking the enzyme with hen egg white using 2% glutaraldehyde. The gel obtained could be lyophilized to give a dry enzyme powder. The pH optimum of both the soluble and immobilized enzyme was found to be 6.8. The immobilized enzyme showed a higher K(m) for the substrates. The extent of enzyme inhibition by galactose was reduced upon immobilization. The stability towards inactivation by heat, urea, gamma irradiation, and protease treatment were enhanced. The bound enzyme as tested in a batch reactor could be used repeatedly for the hydrolysis of milk lactose. The possible application of this system for small-scale domestic use has been suggested.     

Immobilization of fumarase by entrapment of rat liver mitochondria in polyacrylamide gel using gamma rays

A stable immobilized preparation of fumarase (EC 4.2.1.2) was obtained by entrapment of rat liver mitochondria in acrylamide polymerized by using gamma irradiation (100 kR). The enhanced stability and the efficiency of the entrapped enzyme have shown potential for repeated use for the production of L-malic acid from fumaric acid. The possible formation of succinic acid in the system could be controlled by incorporating malonate along with detergents such as sodium deoxycholate or sodium dodecylsulfate in the reactor system.     

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Modification of the radiosensitivity of barley seed by post-treatment with caffein. IV. Effect of the moisture content of seed and storage temperature after irradiation.

The oxygen-dependent damage which develops in barley seeds with approximately 7-8 per cent moisture content disappears after post-irradiation storage in vacuo for 48 hours at 40 degrees C and for 24 hours at 50 degrees C. When the diration of storage at 40 degrees C is extended to 384 hours, oxygen-independent damage becomes potentiated. There is oxygen-dependent damage in seeds of approximately 13.3 per cent moisture content and after the seeds have been stored in vacuo at 50 degrees C, the oxygen-dependent damage begins to increase by 168 hours, and it is very significantly potentiated by 192 hours. Under these circumstances, caffeine acts as a radioprotector only as long as the precursors of oxic damage are present in the seeds. Once these sites are lost, caffeine acts only as a radiosensitizer. The oxygen-independent damage which increases with storage at high temperature is further potentiated by caffeine.     

Volume regulation by flounder red blood cells in anisotonic media

The nucleated high K, low Na red blood cells of the winter flounder demonstrated a volume regulatory response subsequent to osmotic swelling or shrinkage. During volume regulation the net water flow was secondary to net inorganic cation flux. Volume regulation the net water flow was secondary to net inorganic cation flux. Volume regulation after osmotic swelling is referred to as regulatory volume decrease (RVD) and was characterized by net K and water loss. Since the electrochemical gradient for K is directed out of the cell there is no need to invoke active processes to explain RVD. When osmotically shrunken, the flounder erythrocyte demonstrated a regulatory volume increase (RVI) back toward control cell volume. The water movements characteristic of RVI were a consequence of net cellular NaCl and KCl uptake with Na accounting for 75 percent of the increase in intracellular cation content. Since the Na electrochemical gradient is directed into the cell, net Na uptake was the result of Na flux via dissipative pathways. The addition of 10(-4)M ouabain to suspensions of flounder erythrocytes was without effect upon net water movements during volume regulation. The presence of ouabain did however lead to a decreased ration of intracellular K:Na. Analysis of net Na and K fluxes in the presence and absence of ouabain led to the conclusion that Na and K fluxes via both conservative and dissipative pathways are increased in response to osmotic swelling or shrinkage. In addition, the Na and K flux rate through both pump and leak pathways decreased in a parallel fashion as cell volume was regulated. Taken as a whole, the Na and K movements through the flounder erythrocyte membrane demonstrated a functional dependence during volume regulation.