The physiological basis for genetic variation in water use efficiency and carbon isotope composition in Arabidopsis thaliana

Ecologists and physiologists have documented extensive variation in water use efficiency (WUE) in Arabidopsis thaliana, as well as association of WUE with climatic variation. Here, we demonstrate correlations of whole-plant transpiration efficiency and carbon isotope composition (δ¹³C) among life history classes of A. thaliana. We also use a whole-plant cuvette to examine patterns of co-variation in component traits of WUE and δ¹³C. We find that stomatal conductance (g _s) explains more variation in WUE than does A. Overall, there was a strong genetic correlation between A and g _s, consistent with selection acting on the ratio of these traits. At a more detailed level, genetic variation in A was due to underlying variation in both maximal rate of carboxylation (V _cmax) and maximum electron transport rate (Jmax). We also found strong effects of leaf anatomy, where lines with lower WUE had higher leaf water content (LWC) and specific leaf area (SLA), suggesting a role for mesophyll conductance (g _m) in variation of WUE. We hypothesize that this is due to an effect through g _m, and test this hypothesis using the abi4 mutant. We show that mutants of ABI4 have higher SLA, LWC, and g _m than wild-type, consistent with variation in leaf anatomy causing variation in g _m and δ¹³C. These functional data also add further support to the central, integrative role of ABI4 in simultaneously altering ABA sensitivity, sugar signaling, and CO₂ assimilation. Together our results highlight the need for a more holistic approach in functional studies, both for more accurate annotation of gene function and to understand co-limitations to plant growth and productivity.     

Identification of quantitative trait loci for nitrogen use efficiency in maize

Intensively managed crop systems are normally dependent on nitrogen input to maximize yield potential. Improvements in nitrogen- use efficiency (NUE) in crop plants may support the development of cropping systems that are more economically efficient and environment friendly. The objective of this study was to map and characterize quantitative trait loci (QTL) for NUE in a maize population. In preliminary experiments, inbred lines contrasting for NUE were identified and were used to generate populations of F2:3 families for genetic study. A total of 214 F2:3 families were evaluated in replicated trials under high nitrogen (280 kg/ha) and low nitrogen (30 kg/ha) conditions in 1996 and 1997. Analysis of ear-leaf area, plant height, grain yield, ears per plant, kernels number per ear, and kernel weight indicated significant genetic variation among F2:3 families. The heritability of these traits was found to be high (h2=0.57–0.81). The mapping population were genotyped using a set of 99 restriction fragment length polymorphism (RFLP) markers. A linkage map of these markers was developed and used to identify QTL. Between two and six loci were found to be associated with each trait. The correspondence of several genomic regions with traits measured under nitrogen limited conditions suggests the presence of QTL associated with NUE. QTLs will help breeders to improve their maize ideotype of a low-nitrogen efficiency by identifying those constitutive and adaptive traits involved in the expression of traits significantly correlated with yield, such as ear leaf area and number of ears per plant. This revised version was published online in June 2006 with corrections to the Cover Date.     

Towards a better understanding of carotenoid metabolism in animals

Vitamin A derivatives (retinoids) are essential components in vision; they contribute to pattern formation during development and exert multiple effects on cell differentiation with important clinical implications. All naturally occurring vitamin A derives by enzymatic oxidative cleavage from carotenoids with pro-vitamin A activity. To become biologically active, these plant-derived compounds must first be absorbed, then delivered to the site of action in the body, and metabolically converted to the real vitamin. Recently, molecular players of this pathway were identified by the analysis of blind Drosophila mutants. Similar genome sequences were found in vertebrates. Subsequently, these homologous genes were cloned and their gene products were functionally characterized. This review will summarize the advanced state of knowledge about the vitamin A biosynthetic pathway and will discuss biochemical, physiological, developmental and medical aspects of carotenoids and their numerous derivatives.     

Towards a better understanding of agronomic and soil basis for possible charcoal root rot control and production improvement in bean

Abstract

Macrophomina phaseolina causes charcoal root rot (CRR) in numerous crops worldwide. However, structural progression of CRR epidemics in association with bean agro-ecosystems is little understood. Thus, progression of CRR epidemics in interaction with 13 agro-ecological variables was characterised in 48 commercial bean fields. Frequency of pathogen isolated from root was assessed at vegetative (V3), flowering-podding (R6-7) and pod maturity (R9) growth stages. Two principal factors accounting for 89% of total data variance characterised CRR epidemics. Rhizobial nodulation and cultivation–depth, clay–pH, date–preceding crop, urea–bean class and urea–herbicide interactions accounted for 50% CRR epidemic dynamics. Sixty-five percent of production variance was explained by soil clay, bean class, colonisation, planting date and depth, cultivation method, preceding crop, nodulation, herbicide and urea application. The present findings enabled us to explain a noticeable part of variations in productivity among the bean CRR pathosystems with the help of certain agricultural and environmental events for sustainable agriculture purposes.     

An approach to the genetics of nitrogen use efficiency in maize

To study the genetic variability and the genetic basis of nitrogen (N) use efficiency in maize, a set of recombinant inbred lines crossed with a tester was studied at low input (N-) and high input (N+) for grain yield and its components, grain protein content, and post-anthesis nitrogen uptake and remobilization. Other physiological traits, such as nitrate content, nitrate reductase, glutamine synthetase (GS), and glutamate dehydrogenase activities were studied at the level of the lines. Genotypexnitrogen (GxN) interaction was significant for yield and explained by variation in kernel number. In N-, N-uptake, the nitrogen nutrition index, and GS activity in the vegetative stage were positively correlated with grain yield, whereas leaf senescence was negatively correlated. Whatever N-input, post-anthesis N-uptake was highly negatively related to N-remobilization. As a whole, genetic variability was expressed differently in N+ and N-. This was confirmed by the detection of QTLs. More QTLs were detected in N+ than in N- for traits of vegetative development, N-uptake, and grain yield and its components, whereas it was the reverse for grain protein content and N-utilization efficiency. Several coincidences between genes encoding for enzymes of N metabolism and QTLs for the traits studied were observed. In particular, coincidences in three chromosome regions of QTLs for yield and N-remobilization, QTLs for GS activity and a gene encoding cytosolic GS were observed. This may have a physiological meaning. The GS locus on chromosome 5 appears to be a good candidate gene which can, at least partially, explain the variation in nitrogen use efficiency.     

Identification of QTLs associated with physiological nitrogen use efficiency in rice

Demand for low-input sustainable crop cultivation is increasing to meet the need for environment-friendly agriculture. Consequently, developing genotypes with high nutrient use efficiency is one of the major objectives of crop breeding programs. This study was conducted to identify QTLs for traits associated with physiological nitrogen use efficiency (PNUE). A recombinant inbred population (DT-RILs) between Dasanbyeo (a tongil type rice, derived from an indica x japonica cross and similar to indica in its genetic make-up) and TR22183 (a Chinese japonica variety) consisting of 166 F8 lines was developed and used for mapping. A frame map of 1,409 cM containing 113 SSR and 103 STS markers with an average interval of 6.5 cM between adjacent marker loci was constructed using the DT-RILs. The RILs were cultivated in ordinary-N (N-P2O5-K2O = 100-80-80 kg/ha) and low-N (N-P2O5-K2O= 50-80-80 kg/ha) (100 kg/ha) conditions. PNUE was positively correlated with the harvest index and grain yield in both conditions. Twenty single QTLs (S-QTLs) and 58 pairs of epistatic loci (E-QTLs) were identified for the nitrogen concentration of grain, nitrogen concentration of straw, nitrogen content of shoot, harvest index, grain yield, straw yield and PNUE in both conditions. The phenotypic variance explained by these S-QTLs and E-QTLs ranged from 11.1 to 44.3% and from 16.0% to 63.6% , respectively. The total phenotypic variance explained by all the QTLs for each trait ranged from 35.8% to 71.3%, showing that the expression of PNUE and related characters depends significantly upon genetic factors. Both S-QTLs and E-QTLs may be useful for marker-assisted selection (MAS) to develop higher PNUE genotypes.     

Cell biology as the basis of a better understanding of cancer

Clinicians will argue that cancer can only really receive the treatment that is needed through thorough understanding of medicine. However, even empirical approaches to therapy result in experimental analysis of the agencies involved on test cells, usually in culture. From the obverse perspective, cell biologists will argue that until we fully understand cell cycle regulation, tumour management will be too imprecise to make the best advances. A forum is needed whereby the fundamental studies on cells prior to, during and after transformation in vitro can be freely reported (open access) and discussed. The action of anticancer agents and cancer preventative substances can more easily be studied in vitro before the often excessive complexity of making similar studies in experimental and human cancers is tackled. Cancer Cell International is committed to providing such a forum. Ironically within a few months of launching this open access journal, Elsevier had much the same idea, and there one has to pay for the privilege of downloading vital papers in this biomedical field.     

Response of maize genotypes with different nitrogen use efficiency to low nitrogen stresses

Objectives

This paper aims to compare the property difference of spatial and temporal distribution of different nitrogen use efficiency maize genotypes and discuss the physiological mechanism of nitrogen efficiency of maize.

Towards a better understanding of Lactobacillus rhamnosus GG - host interactions

Background

An industrial approach to protein production demands maximization of cloned gene expression, balanced with the recombinant host’s viability. Expression of toxic genes from thermophiles poses particular difficulties due to high GC content, mRNA secondary structures, rare codon usage and impairing the host’s coding plasmid replication. TaqII belongs to a family of bifunctional enzymes, which are a fusion of the restriction endonuclease (REase) and methyltransferase (MTase) activities in a single polypeptide. The family contains thermostable REases with distinct specificities: TspGWI, TaqII, Tth111II/TthHB27I, TspDTI and TsoI and a few enzymes found in mesophiles. While not being isoschizomers, the enzymes exhibit amino acid (aa) sequence homologies, having molecular sizes of ~120 kDa share common modular architecture, resemble Type-I enzymes, cleave DNA 11/9 nt from the recognition sites, their activity is affected by S-adenosylmethionine (SAM).

Results

We describe the taqIIRM gene design, cloning and expression of the prototype TaqII. The enzyme amount in natural hosts is extremely low. To improve expression of the taqIIRM gene in Escherichia coli (E. coli), we designed and cloned a fully synthetic, low GC content, low mRNA secondary structure taqIIRM, codon-optimized gene under a bacteriophage lambda (λ) P _R promoter. Codon usage based on a modified ‘one amino acid–one codon’ strategy, weighted towards low GC content codons, resulted in approximately 10-fold higher expression of the synthetic gene. 718 codons of total 1105 were changed, comprising 65% of the taqIIRM gene. The reason for we choose a less effective strategy rather than a resulting in high expression yields ‘codon randomization’ strategy, was intentional, sub-optimal TaqII in vivo production, in order to decrease the high ‘toxicity’ of the REase-MTase protein.

Conclusions

Recombinant wt and synthetic taqIIRM gene were cloned and expressed in E. coli. The modified ‘one amino acid–one codon’ method tuned for thermophile-coded genes was applied to obtain overexpression of the ‘toxic’ taqIIRM gene. The method appears suited for industrial production of thermostable ‘toxic’ enzymes in E. coli. This novel variant of the method biased toward increasing a gene’s AT content may provide economic benefits for industrial applications.     

Towards a better understanding of the role of psychological variables in arthritis outcome research

In the previous issue of Arthritis Research and Therapy, Brionez and colleagues show that helplessness, depression, and passive coping account for significant variability in self-reported functional limitations in patients with ankylosing spondylitis, beyond the effect of age, inflammation and radiographic damage. Since the perspective of the patients in the experience of health is increasingly important, insight into the type of psychological variables, the pathways by which they influence health and the approaches for how to deal with these variables are challenging.     

Towards understanding the molecular basis of bacterial DNA segregation

Bacteria ensure the fidelity of genetic inheritance by the coordinated control of chromosome segregation and cell division. Here, we review the molecules and mechanisms that govern the correct subcellular positioning and rapid separation of newly replicated chromosomes and plasmids towards the cell poles and, significantly, the emergence of mitotic-like machineries capable of segregating plasmid DNA. We further describe surprising similarities between proteins involved in DNA partitioning (ParA/ParB) and control of cell division (MinD/MinE), suggesting a mechanism for intracellular positioning common to the two processes. Finally, we discuss the role that the bacterial cytoskeleton plays in DNA partitioning and the missing link between prokaryotes and eukaryotes that is bacterial mechano-chemical motor proteins.     

The use of a radial basis neural network and genetic algorithm for improving the efficiency of laccase-mediated dye decolourization

A radial basis function neural network (RBF) and genetic algorithm (GA) were applied to improve the efficiency of the oxidative decolourization of the recalcitrant dye Reactive Black 5 (RB 5) by a technical laccase (Trametes spp.) and the natural mediator acetosyringone (ACS). The decolourization of RB 5 in aqueous solution was studied with a 3(4) factorial design including different levels of laccase (2, 100, 200UL(-1)), acetosyringone (5, 50, 100μM), pH value (3, 4.5, 6) and incubation time (10, 20, 30min). The generated RBF network was mathematically evaluated by several statistical indices and revealed better results than a classical quadratic response surface (RS) model. The experimental data showed that within 10min of incubation time a complete decolourization (>90%) was achieved by using the highest amount of laccase (200UL(-1)) and acetosyringone (100μM) at pH 6. By applying the RBF-GA methodology, the efficiency of the laccase-mediated decolourization was improved by minimising the required amount of laccase and acetosyringone by 25% and 21.7% respectively. Complete decolourization (>90%) was obtained within 10min at the GA-optimised process conditions of laccase (150UL(-1)) and acetosyringone (78.3μM) at pH 5.67. These results illustrate that the RBF-GA methodology could be a powerful technique during scale-up studies.     

Effects of intercropping on photosynthetic rate and net photosynthetic nitrogen use efficiency of maize under nitrogen addition

研究间作后作物光合碳同化和光合氮利用效率(PNUE)对氮投入的响应, 对阐释间作产量优势的氮调控效应, 指导间作氮肥管理有重要意义。本研究设置玉米(Zea mays)单作、玉米间作两种种植模式的4个氮水平(N0, 0 kg·hm ^-2; N1, 125 kg·hm ^-2; N2, 250 kg·hm ^-2; N3, 375 kg·hm ^-2), 分析间作与施氮量对玉米叶片特征、光合参数、PNUE和产量的影响。结果表明: 与单作相比, 间作显著增加玉米叶片的叶干质量和比叶质量; 各施氮水平(除N3)下, 间作中靠近马铃薯(Solanum tuberosum)侧的玉米叶面积均显著高于单作玉米。单间作对比发现, 间作提高了玉米光饱和点和暗呼吸速率。单作、间作靠玉米侧(I-M)、间作靠马铃薯侧(I-P)的玉米PNUE均随施氮量增加而降低, 降幅以I-P最大; 施氮量低于250 kg·hm ^-2时, 相同施氮量下的玉米PNUE和净光合速率(P_n)均以I-P最高, I-M和单作次之。间作显著提高了玉米产量(土地当量比>1)。该研究中当施氮量≤250 kg·hm ^-2时, 间作I-P的玉米叶片P_n和PNUE显著提高可能是间作玉米产量提高的重要原因。     

间作对氮调控玉米光合速率和光合氮利用效率的影响

研究间作后作物光合碳同化和光合氮利用效率(PNUE)对氮投入的响应, 对阐释间作产量优势的氮调控效应, 指导间作氮肥管理有重要意义。本研究设置玉米(Zea mays)单作、玉米间作两种种植模式的4个氮水平(N0, 0 kg·hm ^-2; N1, 125 kg·hm ^-2; N2, 250 kg·hm ^-2; N3, 375 kg·hm ^-2), 分析间作与施氮量对玉米叶片特征、光合参数、PNUE和产量的影响。结果表明: 与单作相比, 间作显著增加玉米叶片的叶干质量和比叶质量; 各施氮水平(除N3)下, 间作中靠近马铃薯(Solanum tuberosum)侧的玉米叶面积均显著高于单作玉米。单间作对比发现, 间作提高了玉米光饱和点和暗呼吸速率。单作、间作靠玉米侧(I-M)、间作靠马铃薯侧(I-P)的玉米PNUE均随施氮量增加而降低, 降幅以I-P最大; 施氮量低于250 kg·hm ^-2时, 相同施氮量下的玉米PNUE和净光合速率(P_n)均以I-P最高, I-M和单作次之。间作显著提高了玉米产量(土地当量比>1)。该研究中当施氮量≤250 kg·hm ^-2时, 间作I-P的玉米叶片P_n和PNUE显著提高可能是间作玉米产量提高的重要原因。     

Genotypic variability for physiological efficiency index of nitrogen in oats

One of the methods for measuring the efficiency of N utilization by plants is the index of physiological efficiency of absorbed N (PEN) which for cereals is defined as the ratio of grain produced to the total N absorbed by the above-ground plant parts (grain and straw) at maturity. This index indicates how this absorbed N is used by the plant to produce grain. The objective of this work was to study the genotypic variability of PEN in oats (Avena sativa L.) and to what extent grain yield is related to PEN. Seven selected oat genotypes were studied under greenhouse conditions with 5 levels of added N including control (no additional N). At maturity the grain and straw were harvested separately and analyzed for total N. The results show that there was a highly significant variation among genotypes in both yield per pot and PEN. Grain yield was positively and significantly related to PEN (r=0.95^xx). The total N absorbed by plants was much less correlated with grain yield than PEN. The results suggest that PEN may be used in a plant breeding program to detect the potentially high yielding oat genotypes and to evaluate those capable of exploiting N input most efficiently.     

Towards an ecological understanding of biological nitrogen fixation

Biogeochemistry - N limitation to primary production and other ecosystem processes is widespread. To understand the causes and distribution of N limitation, we must understand the controls of...