不同施氮量对麦田土壤水稳性团聚体和N2O排放的影响

过量施氮可破坏农田土壤结构,增加温室气体排放量。为揭示不同施氮量对土壤团聚体和N₂O排放的影响,于2018—2020年基于氮肥定位试验,设置秸秆原位还田条件下施氮 0 (N₀)、120 (N₁₂₀)、180 (N₁₈₀)、240 (N₂₄₀)、300 (N₃₀₀)、360 kg·hm^-2 (N₃₆₀) 6个处理,研究不同施氮量对麦田土壤N₂O排放、土壤充水孔隙度(WFPS)、土壤温度、硝态氮、铵态氮含量、水稳性团聚体的组成及稳定性的影响。结果表明: 土壤N₂O排放量与氮肥用量之间呈显著正相关关系,WFPS与施氮量之间无显著相关关系,0~10 cm土壤温度随氮肥施用量的增加而显著降低,土壤硝态氮、铵态氮含量与氮肥施用量间存在显著正相关关系。随氮肥施用量的增加,直径>2 mm的水稳性团聚体含量降低,直径<0.5 mm的水稳性团聚体含量增加,土壤水稳性团聚体的粒径也逐渐减小。氮肥施用量与团聚体平均重量直径(MWD)、几何平均直径之间呈显著负相关关系,但与分形维数之间并无显著相关性。MWD (x)与N₂O排放通量(y)之间的拟合方程为:y=3928.3e^-2.171x (R²=0.55,P<0.001),表明当MWD减小时,N₂O排放量将会剧烈升高。可见,麦田施氮量的增加会降低0~10 cm土壤温度,增加土壤硝态氮和铵态氮含量,减小耕层土壤水稳性团聚体的平均粒径,降低团聚体的稳定性,增加N₂O的排放量。     

CompareSVM: supervised,Support Vector Machine (SVM) inference of gene regularity networks

Background

Predication of gene regularity network (GRN) from expression data is a challenging task. There are many methods that have been developed to address this challenge ranging from supervised to unsupervised methods. Most promising methods are based on support vector machine (SVM). There is a need for comprehensive analysis on prediction accuracy of supervised method SVM using different kernels on different biological experimental conditions and network size.

Results

We developed a tool (CompareSVM) based on SVM to compare different kernel methods for inference of GRN. Using CompareSVM, we investigated and evaluated different SVM kernel methods on simulated datasets of microarray of different sizes in detail. The results obtained from CompareSVM showed that accuracy of inference method depends upon the nature of experimental condition and size of the network.

Conclusions

For network with nodes (<200) and average (over all sizes of networks), SVM Gaussian kernel outperform on knockout, knockdown, and multifactorial datasets compared to all the other inference methods. For network with large number of nodes (~500), choice of inference method depend upon nature of experimental condition. CompareSVM is available at http://bis.zju.edu.cn/CompareSVM/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0395-x) contains supplementary material, which is available to authorized users.     

Radiolabeling and preliminary biodistribution study of 99mTc-labeled antibody-mimetic scaffold protein repebody for initial clearance properties

Antibody-mimetic proteins are intensively being developed for biomedical applications including tumor imaging and therapy. Among them, repebody is a new class of protein that consists of highly diverse leucine-rich repeat (LRR) modules. Although all possible biomedical applications with repebody are ongoing, it’s in vivo biodistribution and excretion pathway has not yet been explored. In this study, hexahistidine (His₆)-tag bearing repebody (rEgH9) was labeled with [^99mTc]-tricarbonyl, and biodistribution was performed following intravenous (I.V.) or intraperitoneal (I.P.) injection. Repebody protein was radiolabeled with high radiolabeling efficiency (>90%) and radiolabeled compound was more than 99% pure after purification. Biodistribution data indicates radiotracer has a rapid clearance from blood and excreted through the kidneys for intravenous (I.V.) injection, but comparatively slow clearance for an intraperitoneal (I.P.) injection. SPECT-CT images were found to be in agreement with biodistribution data, high activity was found inside kidneys. The observed result for rapid blood clearance and renal excretion of repebody (rEgH9) provide useful information for the further development of therapeutic strategy.     

Accurate prediction of protein structural classes using functional domains and predicted secondary structure sequences

Protein structural class prediction is one of the challenging problems in bioinformatics. Previous methods directly based on the similarity of amino acid (AA) sequences have been shown to be insufficient for low-similarity protein data-sets. To improve the prediction accuracy for such low-similarity proteins, different methods have been recently proposed that explore the novel feature sets based on predicted secondary structure propensities. In this paper, we focus on protein structural class prediction using combinations of the novel features including secondary structure propensities as well as functional domain (FD) features extracted from the InterPro signature database. Our comprehensive experimental results based on several benchmark data-sets have shown that the integration of new FD features substantially improves the accuracy of structural class prediction for low-similarity proteins as they capture meaningful relationships among AA residues that are far away in protein sequence. The proposed prediction method has also been tested to predict structural classes for partially disordered proteins with the reasonable prediction accuracy, which is a more difficult problem comparing to structural class prediction for commonly used benchmark data-sets and has never been done before to the best of our knowledge. In addition, to avoid overfitting with a large number of features, feature selection is applied to select discriminating features that contribute to achieve high prediction accuracy. The selected features have been shown to achieve stable prediction performance across different benchmark data-sets.     

Evaluation of infestation percentage of cotton fields to the spiny bollworm,Earias insulana Boisduval (Lep.: Noctuidae), and its relationship with pheromone traps

Spiny bollworm, Earias insulana Boisduval (Lepidoptera: Noctuidae), is one of the most important pest of malvaceous plants throughout the world, except America. In recent years, this insect has been serious pest for cotton fields in southern regions of Iran, especially Darab region of Fars province. In order to evaluate the performance of sex pheromone in reduction of infestation percentage of the spiny bollworm by mass trapping method, an experiment was carried out during year of 2012 in Darab region in Randomised Completely Block Design with six treatments and four replications. The treatments were: application of the four sex pheromone trap densities at the rates of 16, 20, 24 and 30?traps/h, application of Larvin chemical insecticide at the rate of 1?L/h and control. Percentages of infected bolls and flowers to E. insulana were weekly determined. The application of Larvin insecticide performed as the pest population reached to economic threshold level. Analysis variance of results showed that there are significant differences between time, trap number and time?×?trap interaction on infestation percentage per hectare. During sampling time, the highest infestation percentage was in control treatment and the lowest one was observed in 30 and 24?traps/h treatments. The peak of infestation percentage was seen in 18th of November. The best efficiency among treatments was observed in pheromone trap. In conclusion, using sex pheromone trap in comparison to application of insecticides can efficiently reduce infestation level of cotton fields.     

A genomic map of viroid RNA motifs critical for replication and systemic trafficking

RNA replication and systemic trafficking play significant roles in developmental regulation and host-pathogen interactions. Viroids are the simplest noncoding eukaryotic RNA pathogens and genetic units that are capable of autonomous replication and systemic trafficking and offer excellent models to investigate the role of RNA structures in these processes. Like other RNAs, the predicted secondary structure of a viroid RNA contains many loops and bulges flanked by double-stranded helices, the biological functions of which are mostly unknown. Using Potato spindle tuber viroid infection of Nicotiana benthamiana as the experimental system, we tested the hypothesis that these loops/bulges are functional motifs that regulate replication in single cells or trafficking in a plant. Through a genome-wide mutational analysis, we identified multiple loops/bulges essential or important for each of these biological processes. Our results led to a genomic map of viroid RNA motifs that mediate single-cell replication and systemic trafficking, respectively. This map provides a framework to enable high-throughput studies on the tertiary structures and functional mechanisms of RNA motifs that regulate viroid replication and trafficking. Our model and approach should also be valuable for comprehensive investigations of the replication and trafficking motifs in other RNAs.     

Scaffolds derived from cancellous bovine bone support mesenchymal stem cells' maintenance and growth

Since bone defects can lead to various disabilities, in recent years, many increasing attempts have been made in bone tissue engineering. In this regard, scaffolds have attracted a lot of attention as three dimensional substrates for cell attachment which improve successful tissue engineering. The aim of the present study was to provide an interconnected porous scaffold to facilitate cell infiltration. To do so, cancellous bone from bovine femur was dissected in fragments and decellularized by physicochemical methods, including snap freeze/thaw, rinsing in hot water and treatment with different solutions of sodium dodecyl sulfate (SDS). Histological analysis and 4′,6-diamidino-2-phenylindole staining revealed that the best results were obtained after treatment with 2.5%, 5%, and 8% SDS for 8, 3, or 1 h respectively, which significantly removed bone cells with intact trabeculae geometry. Further characterization of decellularized scaffolds by the compression tests also revealed no significant difference between elastic modulus values of the three different SDS treatments. Moreover, studying the ratio of bone trabeculae to bone surfaces (BT/BS) as assessed by Clemex vision software 3.5 showed that treatment with 2.5% SDS for 8 h resulted in a BT/BS score in the range of native bone and therefore this treatment was used for further experiments. Histological studies and scanning electron microscopy revealed rat mesenchymal stem cells integration, adhesion, and maintenance during the 2 and 7 d of culture in vitro. In conclusion, the present results support the effective role of SDS in cancellous bovine bone decellularization and also propensity of treated samples in providing a suitable three-dimentional environment to support the maintenance and growth of mesenchymal stem cells.     

Ligand-based design and synthesis of N'-Benzylidene-3,4-dimethoxybenzohydrazide derivatives as potential antimicrobial agents; evaluation by in vitro,in vivo,and in silico approaches with SAR studies

Herein, a series of N''-benzylidene-3,4-dimethoxybenzohydrazide derivatives were designed and synthesised to target the multidrug efflux pump (MATE). The antibacterial activities were screened against S. aureus, Acinetobacter, S. typhi, E. coli, and P. aeruginosa, whereas their antifungal activities were screened against C. albicans. Compounds 4a, 4h, and 4i showed the most promising antibacterial and antifungal activities. Moreover, compounds 4h and 4i being the broader and superior members regarding their antimicrobial effects were selected to be further evaluated via in vivo testing using biochemical analysis and liver/kidney histological examination. Additionally, molecular docking was carried out to attain further deep insights into the synthesised compounds'' binding modes. Also, ADMET studies were performed to investigate the physicochemical/pharmacokinetics features and toxicity parameters of the synthesised derivatives. Finally, a structure-antimicrobial activity relationship study was established to facilitate further structural modifications in the future.

Highlights

• A series of new N''-benzylidene-3,4-dimethoxybenzohydrazide derivatives were designed and synthesised targeting the multidrug efflux pump (MATE) guided by the pharmacophoric features of the co-crystallized native inhibitor of the target protein.
• The newly synthesised compounds were assessed through in vitro, in vivo, and in silico approaches.
• Using the agar well diffusion assay, the antibacterial activities of the synthesised compounds were screened against S. aureus, Acinetobacter, S. typhi, E. coli, and P. aeruginosa, whereas, their antifungal activities were screened against C. albicans.
• The minimal inhibitory concentration (MIC) and the minimal bactericidal concentration (MBC) of the synthesised compounds were investigated on variable microbial species.
• Compounds (4h and 4i) -as the broader and superior members regarding their antimicrobial effects- were further evaluated via in vivo testing using bio-chemical analysis and liver/kidney histological examination.
• A molecular docking study and ADMET in silico studies were performed.
• A structure-antimicrobial activity relationship study was established to facilitate further structural modifications in the future.

     

Thin layer chromatographical detection of tyrosine produced from <Emphasis Type="SmallCaps">l</Emphasis>-[U-<Superscript>14</Superscript>C]phenylalanine by ruminal microbes

Summary.  Thin layer chromatographical detection of tyrosine (Tyr) synthesized from l-[U-¹⁴C]phenylalanine (Phe) (1 mM) by rumen bacteria (B) and protozoa (P) collected from fistulated Japanese Goat was carried out. About 16 and 12% of the added Phe was converted to Tyr by B and P, respectively. Large amount of radioactivity in ether fractions indicated an abundant production of aromatic acids from Phe. Small amount of radioactivity found in CO₂ fractions implied an occurrence of considerable decarboxylation reaction(s) by rumen bacteria and protozoa. Received July 18, 2001 Accepted December 3, 2001