Hybrid maize breeding with doubled haploids: I. One-stage versus two-stage selection for testcross performance

Optimum allocation of resources is of fundamental importance for the efficiency of breeding programs. The objectives of our study were to (1) determine the optimum allocation for the number of lines and test locations in hybrid maize breeding with doubled haploids (DHs) regarding two optimization criteria, the selection gain ΔG _k and the probability P _k of identifying superior genotypes, (2) compare both optimization criteria including their standard deviations (SDs), and (3) investigate the influence of production costs of DHs on the optimum allocation. For different budgets, number of finally selected lines, ratios of variance components, and production costs of DHs, the optimum allocation of test resources under one- and two-stage selection for testcross performance with a given tester was determined by using Monte Carlo simulations. In one-stage selection, lines are tested in field trials in a single year. In two-stage selection, optimum allocation of resources involves evaluation of (1) a large number of lines in a small number of test locations in the first year and (2) a small number of the selected superior lines in a large number of test locations in the second year, thereby maximizing both optimization criteria. Furthermore, to have a realistic chance of identifying a superior genotype, the probability P _k of identifying superior genotypes should be greater than 75%. For budgets between 200 and 5,000 field plot equivalents, P _k > 75% was reached only for genotypes belonging to the best 5% of the population. As the optimum allocation for P _k (5%) was similar to that for ΔG _k , the choice of the optimization criterion was not crucial. The production costs of DHs had only a minor effect on the optimum number of locations and on values of the optimization criteria. C. Friedrich H. Longin and H. Friedrich Utz contributed equally to this work.     

Screening and molecular dynamics simulation of compounds inhibiting MurB enzyme of drug-resistant Mycobacterium tuberculosis: An in-silico approach

Mycobacterium tuberculosis (MTB) is becoming more and more resistant to drugs and it is a common problem, making current antimicrobials ineffective and highlighting the need for new TB drugs. One of the promising targets for treating MTB is MurB enzymes. This study aimed to identify potential inhibitors of MurB enzymes in M. tuberculosis, as drug resistance among MTB is a significant problem. Attempts are being made to conduct a virtual screening of 30,417 compounds, and thirty-two compounds were chosen for further analysis based on their binding conformations. The selected compounds were assessed for their drug-likeness, pharmacokinetics, and physiochemical characteristics, and seven compounds with binding energy lower than flavin (FAD) were identified. Further, molecular dynamics simulation analysis of these seven compounds found that four of them, namely DB12983, DB15688, ZINC084726167, and ZINC254071113 formed stable complexes with the MurB binding site, exhibiting promising inhibitory activity. These compounds have not been mentioned in any other study, indicating their novelty. The study suggests that these four compounds could be promising candidates for treating MTB, but their effectiveness needs to be validated through in vitro and in vivo experiments. Overall, the findings of this study provide new insight into potential drug targets and candidates for combating drug-resistant MTB.     

Characterizing and modeling hydrogen sulfide production in anaerobic digestion of livestock manure,agro-industrial wastes,and wastewater sludge

Hydrogen sulfide (H₂S) is the most undesirable inorganic gas in biogas from anaerobic digestion (AD). However, H₂S production in AD is complex and understanding of its processes is still limited. This study performed six controlled batch anaerobic co-digestion experiments to investigate H₂S production. Materials were obtained from four field anaerobic digester systems and co-digestion feedstocks from agroindustry. An additional precipitation experiment was conducted to further examine H₂S production dynamics. Digesters containing highly soluble, carbohydrate-based wastes had a high H₂S final specific production (FSP) value. Additionally, the FSP values were negatively correlated with the initial Fe(II):S ratios in the digester liquid of the batch tests. The precipitation experiment indicated that iron sulfide precipitation was preferred in the presence of an anaerobic community. The H₂S production as a time series was successfully modeled using a generalized additive model (R² > 0.82). This study revealed that sulfate, phosphorus, and iron concentrations are important predictors and potential inhibitors of H₂S production in AD. Further examination of real-time H₂S modeling in AD is warranted.     

Mass transfer effects on the reaction rate for heterogeneously distributed immobilized yeast cells

Here we examine the efficiency of different immobilized cell gradients applied to immobilized Saccharomyces cerevisiae fermenting glucose to ethanol. We developed a simulation model to fully study the competing effects of mass transfer hindrance and kinetics. It is based on a diffusion-reaction model and can be used to analyze the different cell concentration profiles inside an immobilized gel bead, in terms of effectiveness factors, productivity, and mass flux. The internal diffusion coefficient, which varies with the local cell concentration, as well as the external mass transfer, is taken into account when describing the efficiency. Although the diffusion hindrance is greater at higher cell concentrations, high cell concentration is still advantageous in the present case because the increase in reaction rate outweighs the diffusion hindrance. Thus, high cell concentrations contribute to increased productivity. The influence of the cell concentration gradient on the efficiency of the beads is negligible. Within the range of cell profiles studied it has been established that the location of the cells within the bead is of lesser importance. However, a steep cell gradient increases the importance of the external mass transfer.     

Increased temperature and precipitation interact to affect root production,mortality, and turnover in a temperate steppe: implications for ecosystem C cycling

Fine root production and turnover play important roles in regulating carbon (C) cycling in terrestrial ecosystems. In order to examine effects of climate change on root production and turnover, a field experiment with increased temperature and precipitation had been conducted in a semiarid temperate steppe in northern China since April 2005. Experimental warming decreased annual root production, mortality, and mean standing crop by 10.3%, 12.1%, 7.0%, respectively, while root turnover was not affected in 2006 and 2007 by the warming. Annual root production and turnover was 5.9% and 10.3% greater in the elevated than ambient precipitation plots. Changes in root production and mortality in response to increased temperature and precipitation could be largely attributed to the changes in gross ecosystem productivity (GEP) and belowground/aboveground C allocation. There were significant interactive effects of warming and increased precipitation on root productivity, mortality, and standing crop. Experimental warming had positive and negative effects on the three root variables (root production, mortality, standing crop) under ambient and increased precipitation, respectively. Increased precipitation stimulated and suppressed the three root variables in the unwarmed and warmed subplots, respectively. The positive dependence of soil respiration and ecosystem respiration upon root productivity and mortality highlights the important role of root dynamics in ecosystem C cycling. The nonadditive effects of increased temperature and precipitation on root productivity, mortality, and standing crop observed in this study are critical for model projections of climate–ecosystem feedbacks. These findings indicate that carbon allocation is a focal point for future research and that results from single factor experiments should be treated with caution because of factor interactions.     

Identification and characterization of key substructures involved in the early folding events of a (beta/alpha)8-barrel protein as studied by experimental and computational methods

A number of studies have examined the structural properties of late folding intermediates of (beta/alpha)8-barrel proteins involved in tryptophan biosynthesis, whereas there is little information available about the early folding events of these proteins. To identify the contiguous polypeptide segments important to the folding of the (beta/alpha)8-barrel protein Escherichia coli N-(5'-phosphoribosyl)anthranilate isomerase, we structurally characterized fragments and circularly permuted forms of the protein. We also simulated thermal unfolding of the protein using molecular dynamics. Our fragmentation experiments demonstrate that the isolated (beta/alpha)(1-4)beta5 fragment is almost as stable as the full-length protein. The far and near-UV CD spectra of this fragment are indicative of native-like secondary and tertiary structures. Structural analysis of the circularly permutated proteins shows that if the protein is cleaved within the two N-terminal betaalpha modules, the amount of secondary structure is unaffected, whereas, when cleaved within the central (beta/alpha)(3-4)beta5 segment, the protein simply cannot fold. An ensemble of the denatured structures produced by thermal unfolding simulations contains a persistent local structure comprised of beta3, beta4 and beta5. The presence of this three-stranded beta-barrel suggests that it may be an important early-stage folding intermediate. Interactions found in (beta/alpha)(3-4)beta5 may be essential for the early events of ePRAI folding if they provide a nucleation site that directs folding.     

荒漠短命植物地上和地下生产力对极端干旱和降水的响应

在古尔班通古特沙漠南缘沙垄4个坡位和坡向,设置减少65%和增加65%生长季降水量以模拟极端干旱和极端降水事件,研究极端干旱和极端降水事件对沙垄不同坡位和坡向短命植物层片生产力的影响。结果表明: 极端干旱使地上净初级生产力和地下净初级生产力分别显著降低48.8%和13.7%,极端降水使地上净初级生产力和地下净初级生产力分别显著增加37.9%和23.2%。地上净初级生产力对极端干旱和极端降水的敏感性(0.26和0.21 g·m^-2·mm^-1)显著强于地下净初级生产力的敏感性(0.02和0.03 g·m^-2·mm^-1)。沙垄东坡地上净初级生产力(24.22 g·m^-2)和地下净初级生产力(5.77 g·m^-2)与西坡相比显著增大29.7%和71.7%,而地上净初级生产力和地下净初级生产力对降水变化的敏感性在不同坡位和坡向之间差异不显著。     

Mathematical simulation of the interactions among cyanobacteria, purple sulfur bacteria and chemotrophic sulfur bacteria in microbial mat communities

Abstract: A deterministic one-dimensional reaction diffusion model was constructed to simulate benthic stratification patterns and population dynamics of cyanobacteria, purple and colorless sulfur bacteria as found in marine microbial mats. The model involves the major biogeochemical processes of the sulfur cycle and includes growth metabolism and their kinetic parameters as described from laboratory experimentation. Hence, the metabolic production and consumption processes are coupled to population growth. The model is used to calculate benthic oxygen, sulfide and light profiles and to infer spatial relationships and interactions among the different populations. Furthermore, the model is used to explore the effect of different abiotic and biotic environmental parameters on the community structure. A strikingly clear pattern emerged of the interaction between purple and colorless sulfur bacteria: either colorless sulfur bacteria dominate or a coexistence is found of colorless and purple sulfur bacteria. The model predicts that purple sulfur bacteria only proliferate when the studied environmental parameters surpass well-defined threshold levels. However, once the appropriate conditions do occur, the purple sulfur bacteria are extremely successful as their biomass outweighs that of colorless sulfur bacteria by a factor of up to 17. The typical stratification pattern predicted closely resembles the often described bilayer communities which comprise a layer of purple sulfur bacteria below a cyanobacterial top-layer; colorless sulfur bacteria are predicted to sandwich in between both layers. The profiles of oxygen and sulfide shift on a diel basis similarly as observed in real systems.     

Effect of filaments within the synaptic cleft on the response of excitatory synapses simulated by computer experiments

Mathematical models of the excitatory synapse are furnishing valuable information about the synaptic response. Based on Brownian-diffusion of glutamate molecules, a synapse model was utilized to investigate the synaptic response on a femto-second time scale by the use of a parallel computer. In particular, the presence of fibrils crossing the synaptic cleft was simulated, which could have a role in shaping the brain activity. To this aim the model of synapse was modified by considering trans-synaptic filaments with diameters ranging from 7 nm to 3 nm, disposed on a grid with spacing of 14 nm or 8 nm. The simulation demonstrated that the presence of filaments induced an increase in the synaptic response, most likely linked to an increment in the probability of encounter between glutamate molecules and receptors. The increase was small - from 5 to 20%, but metabolic and functional considerations provide substantive hints about the importance of these small changes for brain activity. Moreover, it was shown that the presence of filaments made more stable the response of the synapse to random variations of pre-synaptic elements. Originated by these computational results, some inferences about the biological bases of mind diseases such as autism, mental retardation and schizophrenia, are reported in the Discussion.