High-throughput methods for detection of genetic variation

Understanding human genetic variation is currently believed to reveal the cause of individual susceptibility to disease and the large variation observed in response to treatment. In this review, we will focus on different approaches to identify and visualize genetic alterations. The various approaches for allele discrimination are formally systematically divided into (i) enzymatic approaches, in which the properties of different enzymes to discriminate between nucleotides are used (restriction enzymes type II, Cleavase and Resolvase, DNA polymerase, and ligase); (ii) electrophoretic methods, in which the allele discrimination is based on the difference in mobility in polymeric gels or capillaries (single- and double-stranded conformation assays, heteroduplex analysis, and DNA sequencing); (iii) solid-phase determination of allelic variants, including high-density oligonucleotide arrays for hybridization analysis, minisequencing primer extension analysis, and fiberoptic DNA sensor array; (iv) chromatographic methods such as denaturing high-performance liquid chromatography (DHPLC); (v) other physical methods of discrimination of allelic variants such as mass spectrometry (mass and charge) or fluorescence exchange-based techniques; and (vi) in silico methods such as high-throughput analysis of expressed sequence tag data. The most frequently used techniques and instrumental settings applied in different combinations are described, and other methods that are less broadly used but have interesting potentials are discussed.     

A screening method to identify genetic variation in root growth response to a salinity gradient

Salinity as well as drought are increasing problems in agriculture. Durum wheat (Triticum turgidum L. ssp. durum Desf.) is relatively salt sensitive compared with bread wheat (Triticum aestivum L.), and yields poorly on saline soil. Field studies indicate that roots of durum wheat do not proliferate as extensively as bread wheat in saline soil. In order to look for genetic diversity in root growth within durum wheat, a screening method was developed to identify genetic variation in rates of root growth in a saline solution gradient similar to that found in many saline fields. Seedlings were grown in rolls of germination paper in plastic tubes 37 cm tall, with a gradient of salt concentration increasing towards the bottom of the tubes which contained from 50-200 mM NaCl with complete nutrients. Seedlings were grown in the light to the two leaf stage, and transpiration and evaporation were minimized so that the salinity gradient was maintained. An NaCl concentration of 150 mM at the bottom was found suitable to identify genetic variation. This corresponds to a level of salinity in the field that reduces shoot growth by 50% or more. The screen inhibited seminal axile root length more than branch root length in three out of four genotypes, highlighting changes in root system architecture caused by a saline gradient that is genotype dependent. This method can be extended to other species to identify variation in root elongation in response to gradients in salt, nutrients, or toxic elements.     

Bioenergetics and end-product regulation of Clostridium thermosaccharolyticum in response to nutrient limitation

Fermentation of xylose by Clostridium thermosaccharolyticum was studied in batch and continuous culture in which the limiting nutrient was either xylose, phosphate, or ammonia. Transient results obtained in continuous cultures with batch grown inoculum and progressively higher feed substrate concentrations exhibited ethanol selectivities (moles ethanol/moles other products) in excess of 11. The hypothesis that this high ethanol selectivity was a general response to mineral nutrient limitation was tested but could not be supported. Growth and substrate consumption were related by the equation q(s)(1 - Y(x) (c))G(ATP) = (mu/Y(ATP) (max)) + m, with q(s) the specific rate of xylose consumption (moles xylose/hour . g cells), Y(x) (c) the carbon based cell yield (g cell carbon/g substrate carbon), G(ATP) the ATP gain (moles ATP produces/mol substrate catabolized), mu the specific growth rate (1/h), Y(ATP) (max) the ATP-based cell yield (g cells/mol ATP), and m the maintenance coefficient (moles ATP/hour . g cells). Y(ATP) (max) was found to be 11.6 g cells/mol ATP, and m 9.3 mol ATP/hour . g cells for growth on defined medium. Different responses to nutrient limitation were observed depending on the mode of cultivation. Batch and immobilized cell continuous cultures decreased G(ATP) by initiating production of the secondary metabolites, propanediol, and in some cases, D-lactate; in addition, batch cultures increased the fractional allocation of ATP to maintenance and/or wastage. Nitrogen-limited continuous free-cell cultures maintained a constant cell yield, whereas phosphate-limited continuous free-cell cultures did not. In the case of phosphate limitation, the decreased ATP demand associated with the lowered cell yield was accompanied by an increased rate of ATP consumption for maintenance and/or wastage. Neither nitrogen or phosphorus-limited continuous free-cell cultures exhibited an altered G(ATP) in response to mineral nutrient limitation, and neither produced secondary metabolites. (c) 1993 John Wiley & Sons, Inc.     

Aspartokinase II from Bacillus subtilis is degraded in response to nutrient limitation

Aspartokinase II from Bacillus subtilis was shown by immunochemical methods to be regulated by degradation in response to starvation of cells for various nutrients. Ammonium starvation induced the fastest aspartokinase II decline (t1/2 = 65 min), followed by amino acid starvation (t1/2 = 80 min) and glucose limitation (t1/2 = 120 min). Loss of enzyme activity was closely correlated with the disappearance of the alpha subunit; degradation of the beta subunit was somewhat delayed or slower under some conditions. Pulse-chase experiments demonstrated that aspartokinase II was stable during exponential growth; the synthesis of the enzyme rapidly declined in response to nutrient exhaustion. The degradation of aspartokinase II was interrupted by inhibitors of energy production and protein synthesis but was not changed in a mutant lacking a major intracellular protease. Mutants lacking a normal stringent response displayed only a slight decrease in the rate of aspartokinase II degradation, even though aspartate transcarbamylase was degraded more slowly in the same mutant cells. These results indicate that although energy-dependent degradation of biosynthetic enzymes is a general phenomenon in nutrient-starved B. subtilis cells, the degradation of specific enzymes probably involves different pathways.     

Genetic variation in nutrient response functions

Summary Genetic differences in the non-linear growth response function of Pinus sylvestris seedlings to five nutrient levels are analyzed to estimate the causes of variation. Analyses of genotypic differences as quadratic response functions, as stability coefficients, and as separable functions indicate that the estimation of genetic effects can vary widely depending on the analytical model assumed. The existence of different reaction norms is demonstrated.     

Temporal development of the barley leaf metabolic response to Pi limitation

The response of plants to P_i limitation involves interplay between root uptake of P_i, adjustment of resource allocation to different plant organs and increased metabolic P_i use efficiency. To identify potentially novel, early‐responding, metabolic hallmarks of P_i limitation in crop plants, we studied the metabolic response of barley leaves over the first 7 d of P_i stress, and the relationship of primary metabolites with leaf P_i levels and leaf biomass. The abundance of leaf P_i, Tyr and shikimate were significantly different between low Pi and control plants 1 h after transfer of the plants to low P_i. Combining these data with ¹⁵N metabolic labelling, we show that over the first 48 h of P_i limitation, metabolic flux through the N assimilation and aromatic amino acid pathways is increased. We propose that together with a shift in amino acid metabolism in the chloroplast a transient restoration of the energetic and redox state of the leaf is achieved. Correlation analysis of metabolite abundances revealed a central role for major amino acids in P_i stress, appearing to modulate partitioning of soluble sugars between amino acid and carboxylate synthesis, thereby limiting leaf biomass accumulation when external P_i is low.     

Seasonal variation in nutrient limitation of microbial biofilms colonizing organic and inorganic substrata in streams

Humans have increased the availability of nutrients including nitrogen and phosphorus worldwide; therefore, understanding how microbes process nutrients is critical for environmental conservation. We examined nutrient limitation of biofilms colonizing inorganic (fritted glass) and organic (cellulose sponge) substrata in spring, summer, and autumn in three streams in Michigan, USA. Biofilms were enriched with nitrate (NO₃ ⁻), phosphate (PO₄ ³⁻), ammonium (NH₄ ⁺), NO₃ ⁻ + PO₄ ³⁻, NH₄ ⁺ + PO₄ ³⁻, or none (control). We quantified biofilm structure and function as chlorophyll a (i.e., primary producer biomass) and community respiration on all substrata. In one stream, we characterized bacterial and fungal communities on cellulose in autumn using clone library sequencing and denaturing gradient gel electrophoresis to determine if community structure was linked to nutrient limitation status. Despite oligotrophic conditions, primary producer biomass was infrequently nutrient limited. In contrast, respiration on organic substrata was frequently limited by N + P combinations. We found no difference between biofilm response to NH₄ ⁺ versus NO₃ ⁻ enrichment, although the response to both N-species was positively related to water column PO₄ ³⁻ concentrations and temperature. Molecular analysis for fungal community composition suggested no relationship to nutrient limitation, but the dominant members of the bacterial community on cellulose were different on NO₃ ⁻, PO₄³, and NO₃ ⁻ + PO₄ ³⁻ treatments relative to control, NH₄ ⁺, and NH₄ ⁺ + PO₄ ³⁻ treatments, which matched patterns for biofilm respiration rates from each treatment. Our results show discrete patterns of nutrient limitation dependent upon substratum type and season, and imply changes in bacterial community structure and function may be linked following nutrient enrichment in streams.     

Determinants of nutrient limitation in cancer

Proliferation requires that cells accumulate sufficient biomass to grow and divide. Cancer cells within tumors must acquire a variety of nutrients, and tumor growth slows or stops if necessary metabolites are not obtained in sufficient quantities. Importantly, the metabolic demands of cancer cells can be different from those of untransformed cells, and nutrient accessibility in tumors is different than in many normal tissues. Thus, cancer cell survival and proliferation may be limited by different metabolic factors than those that are necessary to maintain noncancerous cells. Understanding the variables that dictate which nutrients are critical to sustain tumor growth may identify vulnerabilities that could be used to treat cancer. This review examines the various cell-autonomous, local, and systemic factors that determine which nutrients are limiting for tumor growth.     

Sex-specific response to nutrient limitation and its effects on female mating success in a gift-giving butterfly

Animals with complex life cycles respond to early food limitation by altering the way resources are allocated in the adult stage. Response to food limitation should differ between males and females, especially in organisms whose mating systems include nutritional nuptial gifts. In these organisms, males are predicted to keep their allocation to reproduction (sperm and nuptial gift production) constant, while females are predicted to sacrifice allocation to reproduction (egg production) since they can compensate by acquiring nuptial gifts when mating. In this study, we investigated how dietary nitrogen limitation during the larval stage affects sex-specific resource allocation in Pieris rapae butterflies. Also, we tested whether nutrient-limited females increased nuptial gift acquisition as a way to compensate for low allocation to reproduction. We found that as predicted females, but not males, sacrifice allocation to reproduction when larval dietary nitrogen is limited. However, females were unable to compensate for this low reproductive allocation by increasing their mating rate to acquire additional gifts. Females reared on low nitrogen diets also reduced wing coloration, a potential signal of female fecundity status. We suggest that female mating frequency is constrained by male mate choice based on females’ wing coloration. This study provides new insights into how larval dietary nitrogen, a key nutritional resource for all herbivores, alters male and female allocation to reproduction as well as to ornamentation.     

A pre‐adaptive approach for tropical forest restoration during climate change using naturally occurring genetic variation in response to water limitation

Effective reforestation of degraded tropical forests depends on selecting planting material suited to the stressful environments typical at restoration sites that can be exacerbated by increased duration and intensity of dry spells expected with climate change. While reforestation efforts in nontropical systems are incorporating drought‐adapted genotypes into restoration programs to cope with drier conditions, such approaches have not been tested or implemented in tropical forests. As the first effort to examine genetic variation in plant response to drought in a tropical wet forest, we established a watering experiment using five replicated maternal lines (i.e. seedlings from different maternal trees) of five dipterocarp species native to Borneo. Apart from the expected species level variation in growth and herbivory (3‐fold variation in both cases), we also found intraspecific variation so that growth in some cases varied 2‐fold, and herbivory 3‐fold, among genetically different maternal lines. In two species we found that among‐maternal line variation in growth rate was negatively correlated with tolerance to water limitation, that is, the maternal lines that performed the best in the high water treatment lost proportionally more of their growth during water limitation. We argue that selection for tolerance to future drier conditions is not only likely to impact population genetics of entire forests, but likely extends from forest trees to the communities of canopy arthropods associated with these trees. In tropical reforestation efforts where increased drought is predicted from climate change, including plant material resilient to drier conditions may improve restoration effectiveness.     

High-throughput screening of microbial adaptation to environmental stress

We developed a microwell plate, high-throughput, screening method aimed at quantitating the tolerance of a panel of Gram-positive and Gram-negative bacteria to metals (Frankia sp., Escherichia coli, Cupriavidus metallidurans, Rhizobium leguminosarum, and Streptomyces scabies). Microbial viability was quantified using MTS; a tetrazolium salt converted to a water-soluble formazan through microbial reduction. In this paper, we present the stepwise development of the method, highlighting the main elements underlying its reliability, and compare results obtained with literature. We conclude the method is well suited to efficiently screen bacteria, including those that are filamentous and slow-growing, without the need for large amounts of inoculum which may not always be available. The method allows testing of compound gradients with sufficient replicates to generate statistically robust results, and is transposable to other types of cell proliferation assays such as those for antimicrobial susceptibility, and chemoresistance.     

Experiments on nutrient limitation in bottles

A simple model is used to illustrate the character of production,within an incubation bottle subject to addition of a potentiallylimiting nutrient, over time periods long relative to the algaldynamics (1–10 days). Grazing by microheterotrophs significantlyaffects algal and nutrient dynamics, and production reflectsthe integration over time of grazing and nutrient-regulatedgrowth. Greater production is found with increased nutrient,but this increase continues into the region of luxuriant nutrient.Increased production per se cannot be used to determine whethera nutrient is limiting.     

Mechanisms of response to salinity in halotolerant microalgae

Summary A limited number of organic solutes are used by microalgae to adjust their internal osmotic pressure in response to changing external salinities. Glycerol and proline are used by the most extremely halotolerant algae. Only glycerol allows growth at salinities approaching saturation. In addition to organic osmoregulatory solutes, inorganic ions also play an important role in osmoregulation. The ability of microalgae to maintain intracellular ions at levels compatible with metabolic functions may set upper limits for their salt tolerance. Requirements for NaCl in the external medium for nutrient transport may define the lower salinity limits for growth observed for some euryhaline algae.Osmotic upshocks generally cause severe temporary inhibition of photosynthesis in euryhaline microalgae. Extensive osmotic downshocks have little effect on photosynthesis in microalgae with strong cell walls, while wall-less species appear to be more sensitive. Rapid glycerol synthesis takes place in response to increased external salinity inChlamydomonas pulsatilla both in light and dark. Starch supplies carbon for glycerol synthesis in the dark and also during the initial periods of inhibition of photosynthesis in the light. Turnover of osmoregulatory solutes such as glycerol and isofloridoside may be an important aspect of the osmoregulatory mechanism.At salinities beyond the growth limit for the green flagellateChlamydomonas pulsatilla, resting spores are formed that enable this alga to survive extreme salinities.     

Seed size and seedling growth: differential response of Australian and British Fabaceae to nutrient limitation

Seed size is widely held to exert an important influence over plant establishment, but while large seeds are often assumed to be at an advantage in nutrient-limited conditions, there is in fact, little consistent evidence to support this hypothesis. Here, we examined the interspecific relationship between seedling growth and seed size for Australian and British Fabaceae species in nutrient solutions deficient in nitrogen, phosphorus, potassium or all nutrients combined (distilled water). The British species showed no consistent link between mean seed mass and seedling growth in nutrient-limited conditions. By contrast, all four nutrient-deficient treatments yielded a significant relationship for the Australian species. Linear regression showed that growth under balanced nutrient conditions was positively associated with growth without nutrients, although in fewer cases for the British species. We suggest that habitat-specific differences in regeneration conditions and/or evolutionary history may influence the role that seed size plays in dictating how seedlings of different species respond to nutrient shortage. We recommend caution in attempts to link traits like seed size to wider patterns of plant community ecology.     

Transient response of Enterobacter aerogenes under a dual nutrient limitation in a chemostat.

Utilizing a chemostat with a dual nutrient limitation of nitrogen and phosphate, we examined the transient response of the culture following a pulse of one of the limiting nutrients (ammonia). This method provided quantitative evidence that cells can be grown under dual nutrient limitation. Furthermore, the pattern of response was consistent with the hypothesis that phosphate limitation restricts nucleic acid synthesis in the cell and that nitrogen limitation restricts protein synthesis. The net result is that under a phosphate limitation there is a restricted biosynthetic capacity which we feel is closely associated with the RNA content of the cell.