QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight functionalities are ...integrated in this software package: (1) BIN: binning of redundant markers; (2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sharing common markers; (4) SDL: mapping of segregation distortion loci; (5) BIP: mapping of additive, dominant, and digenic epistasis genes; (6) MET: QTL-by-environment interaction analysis; (7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials.
A novel graphene-copper nanoparticle composite was prepared by the in situ chemical reduction of a mixture containing graphene oxide and copper(II) ions using potassium borohydride as a reductant. It ...was mixed with paraffin oil and packed into one end of a fused capillary to fabricate microdisc electrodes for sensing carbohydrates. The morphology and structure of the graphene-copper nanoparticle composite were investigated by scanning electron microscopy, X-ray diffraction, and Fourier transform-infrared spectroscopy. The results indicated that copper nanoparticles with an average diameter of 20.8 nm were successfully deposited on graphene nanosheets to form a well interconnected hybrid network. The analytical performance of these unique graphene-copper nanoparticle composite paste electrodes was demonstrated by sensing five carbohydrates in combination with cyclic voltammetry and capillary electrophoresis (CE). The advantages of the composite detectors include higher sensitivity, satisfactory stability, surface renewability, bulk modification, and low expense of fabrication. They should find applications in microchip CE, flowing-injection analysis, and other microfluidic analysis systems.
Identification of environment-specific QTL and stable QTL having consistent genetic effects across a wide range of environments is of great importance in plant breeding. Inclusive Composite Interval ...Mapping (ICIM) has been proposed for additive, dominant and epistatic QTL mapping in biparental populations for single environment. In this study, ICIM was extended to QTL by environment interaction (QEI) mapping for multi-environmental trials, where the QTL average effect and QEI effects could be properly estimated. Stepwise regression was firstly applied in each environment to identify the most significant marker variables which were then used to adjust the phenotypic values. One-dimensional scanning was then conducted on the adjusted phenotypic values across the environments in order to detect QTL with either average effect or QEI effects, or both average effect and QEI effects. In this way, the genetic background could be well controlled while the conventional interval mapping was applied. An empirical method to determine the threshold of logarithm of odds was developed, and the efficiency of the ICIM QEI mapping was demonstrated in simulated populations under different genetic models. One actual recombinant inbred line population was used to compare mapping results between QEI mapping and single-environment analysis.
Residual pharmaceuticals have received widespread attention worldwide due to their continuous release and potential hazard to the environment. As a result of rapid development and a large population, ...China has become a country with high production and consumption of pharmaceuticals. This may be the main reason for the high detection frequencies and concentrations of pharmaceuticals in the aquatic environment in China. Rivers represent an important water resource and play an important role in the sustainable development of the Chinese economy and society. This study summarizes the occurrence of frequently detected pharmaceuticals in major rivers. A hazard score based on the occurrence, exposure potential, and environmental effects of pharmaceuticals was calculated and a prioritization approach was used to rank 166 pharmaceuticals that were detected in the aquatic environment of major rivers in China. The priority list provides a basis for selecting candidate pharmaceuticals for future site-specific monitoring in rivers.
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•Regional distribution of 166 pharmaceuticals in major rivers in China was studied.•Pharmaceutical ranking list was determined based on three criteria.•A priority list of fourteen pharmaceuticals was identified.•The highest hazardous risk of pharmaceuticals was found in Pearl River.
Genomic selection (GS) is a strategy to predict the genetic merits of individuals using genome-wide markers. However, GS prediction accuracy is affected by many factors, including missing rate and ...minor allele frequency (MAF) of genotypic data, GS models, trait features, etc. In this study, we used one wheat population to investigate prediction accuracies of various GS models on yield and yield-related traits from various quality control (QC) scenarios, missing genotype imputation, and genome-wide association studies (GWAS)-derived markers. Missing rate and MAF of single nucleotide polymorphism (SNP) markers were two major factors in QC. Five missing rate levels (0%, 20%, 40%, 60%, and 80%) and three MAF levels (0%, 5%, and 10%) were considered and the five-fold cross validation was used to estimate the prediction accuracy. The results indicated that a moderate missing rate level (20% to 40%) and MAF (5%) threshold provided better prediction accuracy. Under this QC scenario, prediction accuracies were further calculated for imputed and GWAS-derived markers. It was observed that the accuracies of the six traits were related to their heritability and genetic architecture, as well as the GS prediction model. Moore-Penrose generalized inverse (GenInv), ridge regression (RidgeReg), and random forest (RForest) resulted in higher prediction accuracies than other GS models across traits. Imputation of missing genotypic data had marginal effect on prediction accuracy, while GWAS-derived markers improved the prediction accuracy in most cases. These results demonstrate that QC on missing rate and MAF had positive impact on the predictability of GS models. We failed to identify one single combination of QC scenarios that could outperform the others for all traits and GS models. However, the balance between marker number and marker quality is important for the deployment of GS in wheat breeding. GWAS is able to select markers which are mostly related to traits, and therefore can be used to improve the prediction accuracy of GS.
This study used large-scale time-varying network analysis to reveal the diverse network patterns during the different decision stages and found that the responses of rejection and acceptance involved ...different network structures. When participants accept unfair offers, the brain recruits a more bottom-up mechanism with a much stronger information flow from the visual cortex (O2) to the frontal area, but when they reject unfair offers, it displayed a more top-down flow derived from the frontal cortex (Fz) to the parietal and occipital cortices. Furthermore, we performed 2 additional studies to validate the above network models: one was to identify the 2 responses based on the out-degree information of network hub nodes, which results in 70% accuracy, and the other utilized theta burst stimulation (TBS) of transcranial magnetic stimulation (TMS) to modulate the frontal area before the decision-making tasks. We found that the intermittent TBS group demonstrated lower acceptance rates and that the continuous TBS group showed higher acceptance rates compared with the sham group. Similar effects were not observed after TBS of a control site. These results suggest that the revealed decision-making network model can serve as a potential intervention model to alter decision responses.
From bi-parental pure-inbred lines (PIL), immortalized backcross (i.e., IB
and IB
, representing the two directions of backcrossing) and F
(i.e., IF
) populations can be developed. These populations ...are suitable for genetic studies on heterosis, due to the present of both homozygous and heterozygous genotypes, and in the meantime allow repeated phenotyping trials across multiple locations and years. In this study, we developed a combined approach of quantitative trait locus (QTL) mapping, when some or all of the four immortalized populations (i.e., PIL, IB
, IB
, and IF
) are available. To estimate the additive and dominant effects simultaneously and accurately, suitable transformations are made on phenotypic values from different populations. When IB
and IB
are present, summation and subtraction are used. When IF
and PIL are available, mid-parental values and mid-parental heterosis are used. One-dimensional genomic scanning is performed to detect the additive and dominant QTLs, based on the algorithm of inclusive composite interval mapping (ICIM). The proposed approach was applied to one IF
population together with PIL in maize, and identified ten QTLs on ear length, showing varied degrees of dominance. Simulation studies indicated the proposed approach is similar to or better than individual population mapping by QTL detection power, false discovery rate (FDR), and estimated QTL position and effects.
GAHP is a freely available software package for genetic analysis with bi-parental immortalized heterozygous and pure-line populations. The package is project-based and integrated with multiple ...functions. All operations and running results are properly saved in a project, which can be recovered when the project is re-open by the package. Four functionalities have been implemented in the current version of GAHP, i.e., 1) MHP: visualization of genetic linkage maps; 2) VHP: analysis of variance (ANOVA) and estimation of heritability on phenotypic data; 3) QHP: quantitative trait locus (QTL) mapping on both genotypic and phenotypic data; 4) SHP: simulation of bi-parental immortalized heterozygous and pure-line populations, and power analysis of QTL mapping. VHP and QHP can be conducted in individual populations, as well as in multiple populations by the combined analysis. Input files are arranged either in the plain text format with an extension name same as the functionality or in the MS Excel formats. Output files have the same prefix name as the input file, but with different extensions to indicate their contents. Three characters before the extension names stand for the types of populations used in analysis. In the interface of the software package, input files are grouped by functionality, and output files are grouped by individual or combined mapping populations. In addition to the text-format outputs, the constructed linkage map can be visualized per chromosome or for a number of selected chromosomes; line plots and bi-plots can be drawn from QTL mapping results and phenotypic data. Functionalities and analysis methods available in GAHP help the investigation of genetic architectures of complex traits and the mechanism of heterosis in plants.
Carbon nanotube-nickel nanoparticle (CNT-NiNP) hybrid was prepared by the chemical reduction of a mixture containing nickel sulfate and CNTs using hydrazine. The structure of the material was ...characterized by scanning electron microscopy, energy dispersive spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, and vibrating sample magnetometery. A mixture of the CNT-NiNP hybrid and paraffin oil was packed into fused capillaries to fabricate paste electrodes for electrochemical sensing. The performance of the fabricated electrodes was demonstrated by measuring four carbohydrates in combination with cyclic voltammetry and capillary electrophoresis. The advantages of the electrodes include higher sensitivity, satisfactory stability, surface renewability, and low expense of fabrication. They may find wide applications in microchip capillary electrophoresis, flowing-injection analysis, and other microfluidic analysis systems.
Poly(methyl methacrylate) (PMMA) is particularly useful for microfluidic chips with the features of low price, excellent optic transparency, attractive mechanical and chemical properties, ease of ...fabrication and modification, biocompatibility, etc. During the past decade, significant progress in the PMMA microfluidic chips has occurred. This review, which contains 120 references, summarizes the recent advances and the key strategies in the fabrication, modification, and application of PMMA microfluidic chips. It is expected that PMMA microchips should find a wide range of applications and will lead to the creation of truly disposable microfluidic devices.
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