AhDMT1, a Fe<Superscript>2+</Superscript> transporter,is involved in improving iron nutrition and N<Subscript>2</Subscript> fixation in nodules of peanut intercropped with maize in calcareous soils

Peanut (Arachis hypogaea L.) is an important legume providing edible proteins and N₂ fixation. However, iron deficiency severely reduces peanut growth in calcareous soils. The maize/peanut intercropping effectively improves iron nutrition and N₂ fixation of peanut under pot and field conditions on calcareous soils. However, little was known of how intercropping regulates iron transporters in peanut. We identified AhDMT1 as a Fe²⁺ transporter which was highly expressed in mature nodules with stronger N₂ fixation capacity. Promoter expression analysis indicated that AhDMT1 was localized in the vascular tissues of both roots and nodules in peanut. Short-term Fe-deficiency temporarily induced an AhDmt1 expression in mature nodules in contrast to roots. However, analysis of the correlation between the complex regulation pattern of AhDmt1 expression and iron nutrition status indicated that sufficient iron supply for long term was a prerequisite for keeping AhDmt1 at a high expression level in both, peanut roots and mature nodules. The AhDmt1 expression in peanut intercropped with maize under 3 years greenhouse experiments was similar to that of peanut supplied with sufficient iron in laboratory experiments. Thus, the positive interspecific effect of intercropping may supply sufficient iron to enhance the expression of AhDmt1 in peanut roots and mature nodules to improve the iron nutrition and N₂ fixation in nodules. This study may also serve as a paradigm in which functionally important genes and their ecological significance in intercropping were characterized using a candidate gene approach.     

Salinity induced the changes of root growth and antioxidative responses in two wheat cultivars

This study aimed to investigate the inhibitory mechanism of root growth and to compare antioxidative responses in two wheat cultivars, drought-tolerant Ningchun and drought-sensitive Xihan, exposed to different NaCl concentrations. Ningchun exhibited lower germination rate, seedling growth, and lipid peroxidation than Xihan when exposed to salinity. The loss of cell viability was correlated with the inhibition of root growth induced by NaCl stress. Moreover, treatments with H₂O₂ scavenger dimethylthiourea and catalase (CAT) partly blocked salinity-induced negative effects on root growth and cell viability. Besides, the enhancement of superoxide radical and H₂O₂ levels, and the stimulation of CAT and diamine oxidase (DAO) as well as the inhibition of glutathione reductase (GR) were observed in two wheat roots treated with salinity. However, hydroxyl radical content increased only in Xihan roots under NaCl treatment, and the changes of soluble peroxidase (POD), ascorbate peroxidase (APX), superoxide dismutase (SOD), and cell-wall-bound POD activities were different in drought-tolerant Ningchun and drought-sensitive Xihan exposed to different NaCl concentrations. In conclusion, salinity might induce the loss of cell viability via a pathway associated with extracellular H₂O₂ generation, which was the primary reason leading to the inhibition of root growth in two wheat cultivars. Here, it was also suggested that increased H₂O₂ accumulation in the roots of drought-tolerant Ningchun might be due to decreased POD and GR activities as well as enhanced cell-wall-bound POD and DAO ones, while the inhibition of APX and GR as well as the stimulation of SOD and DAO was responsible for the elevation of H₂O₂ level in drought-sensitive Xihan roots.     

Photosynthesis and chlorophyll fluorescence response to low sink demand of tubers and roots in <Emphasis Type="Italic">Dahlia pinnata</Emphasis> source leaves

Photosynthetic rate (P_N) and chlorophyll (Chl) fluorescence induction of source leaves in response to a low sink demand created by girdling the branch (GB) between the root-tuber-system and the leaves were studied in Dahlia pinnata L. cv. Rigolet during the stage of rapid tuber growth in the greenhouse. GB resulted in significantly lower values of P_N, stomatal conductance (g_s), and transpiration rate (E), but in higher leaf temperature (T_l) compared with those of controls. With exception of maximum quantum yield of photosystem 2 (PS 2) photochemistry (F_v/F_m) and maximum ratio of quantum yields of photochemical and concurrent non-photochemical processes in PS 2 (F_v/F₀), no significant differences were observed in Chl fluorescence parameters between girdled and control leaves on days 1 and 2 after GB, indicating no apparent damage in the photosynthetic apparatus. However, longer girdling duration resulted in higher non-photochemical Chl fluorescence quenching (NPQ), but lower F_v/F₀, actual efficiency of energy conversion in PS 2 under steady-state conditions (Φ_PS2), and photochemical quenching coefficient (qP) in comparison with controls from 10:00 to 16:00 or 15:00 on days 4 and 5, respectively, indicating reversible injury in the photosynthetic apparatus.     

Prediction-based structured variable selection through the receiver operating characteristic curves

In many clinical settings, a commonly encountered problem is to assess accuracy of a screening test for early detection of a disease. In these applications, predictive performance of the test is of interest. Variable selection may be useful in designing a medical test. An example is a research study conducted to design a new screening test by selecting variables from an existing screener with a hierarchical structure among variables: there are several root questions followed by their stem questions. The stem questions will only be asked after a subject has answered the root question. It is therefore unreasonable to select a model that only contains stem variables but not its root variable. In this work, we propose methods to perform variable selection with structured variables when predictive accuracy of a diagnostic test is the main concern of the analysis. We take a linear combination of individual variables to form a combined test. We then maximize a direct summary measure of the predictive performance of the test, the area under a receiver operating characteristic curve (AUC of an ROC), subject to a penalty function to control for overfitting. Since maximizing empirical AUC of the ROC of a combined test is a complicated nonconvex problem (Pepe, Cai, and Longton, 2006, Biometrics62, 221-229), we explore the connection between the empirical AUC and a support vector machine (SVM). We cast the problem of maximizing predictive performance of a combined test as a penalized SVM problem and apply a reparametrization to impose the hierarchical structure among variables. We also describe a penalized logistic regression variable selection procedure for structured variables and compare it with the ROC-based approaches. We use simulation studies based on real data to examine performance of the proposed methods. Finally we apply developed methods to design a structured screener to be used in primary care clinics to refer potentially psychotic patients for further specialty diagnostics and treatment.     

Rationalizing 5000-fold differences in receptor-binding rate constants of four cytokines

The four cytokines erythropoietin (EPO), interleukin-4 (IL4), human growth hormone (hGH), and prolactin (PRL) all form four-helix bundles and bind to type I cytokine receptors. However, their receptor-binding rate constants span a 5000-fold range. Here, we quantitatively rationalize these vast differences in rate constants by our transient-complex theory for protein-protein association. In the transient complex, the two proteins have near-native separation and relative orientation, but have yet to form the short-range specific interactions of the native complex. The theory predicts the association rate constant as where k_a0 is the basal rate constant for reaching the transient complex by random diffusion, and the Boltzmann factor captures the rate enhancement due to electrostatic attraction. We found that the vast differences in receptor-binding rate constants of the four cytokines arise mostly from the differences in charge complementarity among the four cytokine-receptor complexes. The basal rate constants (k_a0) of EPO, IL4, hGH, and PRL were similar (5.2 × 10⁵ M⁻¹s⁻¹, 2.4 × 10⁵ M⁻¹s⁻¹, 1.7 × 10⁵ M⁻¹s⁻¹, and 1.7 × 10⁵ M⁻¹s⁻¹, respectively). However, the average electrostatic free energies () were very different (−4.2 kcal/mol, −2.4 kcal/mol, −0.1 kcal/mol, and −0.5 kcal/mol, respectively, at ionic strength = 160 mM). The receptor-binding rate constants predicted without adjusting any parameters, 6.2 × 10⁸ M⁻¹s⁻¹, 1.3 × 10⁷ M⁻¹s⁻¹, 2.0 × 10⁵ M⁻¹s⁻¹, and 7.6 × 10⁴ M⁻¹s⁻¹, respectively, for EPO, IL4, hGH, and PRL agree well with experimental results. We uncover that these diverse rate constants are anticorrelated with the circulation concentrations of the cytokines, with the resulting cytokine-receptor binding rates very close to the limits set by the half-lives of the receptors, suggesting that these binding rates are functionally relevant and perhaps evolutionarily tuned. Our calculations also reproduced well-observed effects of mutations and ionic strength on the rate constants and produced a set of mutations on the complex of hGH with its receptor that putatively enhances the rate constant by nearly 100-fold through increasing charge complementarity. To quantify charge complementarity, we propose a simple index based on the charge distribution within the binding interface, which shows good correlation with . Together these results suggest that protein charges can be manipulated to tune k_a and control biological function.     

Alzheimer's Disease Drug Candidates Stabilize A-β Protein Native Structure by Interacting with the Hydrophobic Core

Deposition of amyloid fibrils, consisting primarily of Aβ₄₀ and Aβ₄₂ peptides, in the extracellular space in the brain is a major characteristic of Alzheimer's disease (AD). We recently developed new (to our knowledge) drug candidates for AD that inhibit the fibril formation of Aβ peptides and eliminate their neurotoxicity. We performed all-atom molecular-dynamics simulations on the Aβ₄₂ monomer at its α-helical conformation and a pentamer fibril fragment of Aβ₄₂ peptide with or without LRL and fluorene series compounds to investigate the mechanism of inhibition. The results show that the active drug candidates, LRL22 (EC₅₀ = 0.734 μM) and K162 (EC₅₀ = 0.080 μM), stabilize hydrophobic core I of Aβ₄₂ peptide (residues 17–21) to its α-helical conformation by interacting specifically in this region. The nonactive drug candidates, LRL27 (EC₅₀ > 10 μM) and K182 (EC₅₀ > 5 μM), have little to no similar effect. This explains the different behavior of the drug candidates in experiments. Of more importance, this phenomenon indicates that hydrophobic core I of the Aβ₄₂ peptide plays a major mechanistic role in the formation of amyloid fibrils, and paves the way for the development of new drugs against AD.     

Enzymatic synthesis of L‐lactic acid from carbon dioxide and ethanol with an inherent cofactor regeneration cycle

Efficient conversion of carbon dioxide is of great interests to today's endeavors in controlling greenhouse gas emission. A multienzyme catalytic system that uses carbon dioxide and ethanol to produce L ‐lactate was demonstrated in this work, thereby providing a novel reaction route to convert bio‐based ethanol to an important building block for synthesis biodegradable polymers. The synthetic route has a unique internal cofactor regeneration cycle, eliminating the need of additional chemical or energy for cofactor regeneration. Lactate was successfully synthesized with 41% of ethanol converted in a batch reaction, while a turnover number of 2.2 day⁻¹ was reached for cofactor regeneration in a reaction with continuous feeding of ethanol. A kinetic model developed based on reaction kinetic parameters determined separately for each reaction step predicted well the reaction rates and yields of the multienzyme reaction system. Biotechnol. Bioeng. 2011;108: 465–469. © 2010 Wiley Periodicals, Inc.