An innovative approach for testing bioinformatics programs using metamorphic testing

Background  

Recent advances in experimental and computational technologies have fueled the development of many sophisticated bioinformatics programs. The correctness of such programs is crucial as incorrectly computed results may lead to wrong biological conclusion or misguide downstream experimentation. Common software testing procedures involve executing the target program with a set of test inputs and then verifying the correctness of the test outputs. However, due to the complexity of many bioinformatics programs, it is often difficult to verify the correctness of the test outputs. Therefore our ability to perform systematic software testing is greatly hindered.     

Ion Compartmentation in the Marine Fungus Dendryphiella salina in Response to Salinity: X-ray Microanalysis

X-ray microanalysis was performed on hyphae of the filamentousmarine fungus Dendryphiella salina growing at different salinitiesto give sodium, potassium and chloride concentrations in thecytoplasm, vacuole and cell wall. Sodium and chloride concentrationsincreased with salinity in all compartments. Cytoplasmic andvacuolar sodium and chloride concentration were broadly similar,and vacuolar contents represented, at most, 19% of the totalprotoplasmic content of an individual ion species. Potassiumconcentrations decreased to some extent with salinity, althoughconcentrations were not severely affected by competition withsodium uptake. Results are discussed with regard to the roleof ions in the overall osmotic adjustment in this species. Key words: Dendryphiella salina, marine fungus, salt-tolerance, x-ray microanalysis     

THE EFFECTS OF SODIUM CHLORIDE ON HIGHER PLANTS

(1) This review concentrates on the effect of sodium chloride on the growth of higher plants, being primarily concerned with relatively high concentrations i.e. 50 mmol 1^-1 and above, though something is also said about those instances when sodium acts as a micronutrient. Emphasis is placed on particular species or genera for which enough information is available to discuss possible mechanisms. (2) Trace amounts of sodium are required for the growth of plants using the C₄ pathway of carbon fixation and may also be important in plants with Crassulacean acid metabolism. (3) The increased growth of Beta vulgaris brought about by sodium chloride can in part be explained by a sparing effect on potassium. However, growth is still increased when sufficient potassium is available. Complementary studies with rubidium indicate that the hormone balance in the plant may be changed. Sodium chloride also increases the level of sucrose in storage roots and allows beet plants to withstand water stress more readily, possibly by increased turgor pressure. (4) Sodium chloride increases production of dry matter in C₄ species of Atriplex under conditions of low relative humidity because water loss is reduced and photo-synthesis hardly affected. (5) Succulence in many plants is stimulated by salinity. The essential basis of the phenomenon is an increased water potential gradient between the leaf and the external medium. In some instances, it is the accumulation of chloride which is important; in others it is the accumulation of cations, when potassium can be as effective as sodium. (6) Salinity reduces the final area achieved by growing leaves. Most of the studies have been made on Phaseolus vulgaris and an important early event is the reduction in the rate of expansion of the epidermal cells and this may be accompanied by a decrease in their number. Reduction of epidermal cell size is a result of water stress; sodium chloride may directly affect cell division, though water stress cannot be ruled out. Whether salinity brings about inhibition of cell division depends upon the calcium content of the medium – a high content is accompanied solely by a reduction in epidermal cell size. (7) Hormones, as yet unspecified, may play an important part in response of a growing leaf to salinity. However, there is no evidence that sodium chloride per se has an effect on hormone balance within the plant. So far, any measured changes in levels of specific hormones can be ascribed to the osmotic effects of the saline medium. (8) Two estimates by flux analysis of cytoplasmic concentration of sodium in plants growing in conditions of high salinity give a value of around 150 mmol 1^-1. There is no similar information for chloride. Other techniques (histochemistry and X-ray micro-probe analysis) give questionable information. (9) There is now extensive information to show that enzymes of halophytes (other than ATPases) do not differ significantly from those of other higher plants with respect to their sensitivity in vitro to sodium chloride. There is a need for further work with respect to the activity of enzymes in the presence of those metabolites which have the highest cytoplasmic concentration. (10) Sodium-stimulated ATPases have been isolated from plant cells but their distribution amongst higher plants is restricted. (11) There are a number of reports of changed metabolism brought about by saline treatments but it is not clear how far the effects of sodium chloride and water stress are confounded. (12) Sodium appears to increase the sucrose levels in sugar beet by an inhibitory effect on product starch-granule-bound ADP-glucose starch synthase. (13) Reversal of a sodium pump located at the plasmalemma might have an effect on cell turgor. (14) Sodium (like other monovalent cations) causes loss of materials from plant cells, possibly through an effect on carrier proteins; calcium prevents this from happening. Calcium also allows plants to grow better in saline conditions by a depression of sodium uptake by and transport within the plant. The properties and composition of the membranes of mesophytes and halophytes need to be compared. (15) A saline medium exerts a major effect on plant growth through water stress to which a halophyte must adapt. As well as this, the cytoplasmic concentration of sodium chloride must be kept lower than the total cellular concentration of the salt. Unless this happens, it is likely that enzymic activity will be reduced due, in some instances, to an unspecific effect of a high concentration of monovalent cations and/or chloride and in other instances to competition between sodium and other cations, specifically potassium, for activation sites on enzymes, e.g. pyruvate kinase. (16) Further work is required to separate the osmotic effects from the specific effect of sodium chloride after it has entered the plant. As well as this, it has become clear that more information is needed about the mineral nutrition of halophytes.