CH4 emissions from rice paddies managed according to farmer's practice in Hunan, China

We measured CH₄ emissions from ricepaddies managed by farmer's practices inChangsha, Hunan Province, China, from 1995 to1997. During the winter season, rice fieldswere left fallow under either drained(C-Fallow) or flooded conditions (C-Flood), andplanted with either Chinese milk vetch (C-GM)or oil-seed rape (C-Rape). The organic manureproduced in the winter (weeds, Chinese milkvetch, or oil-seed rape straw) was incorporatedin situ before the early-ricetransplanting. Both early-rice and late-ricestraws were removed and the soil was notamended with any exogenous organic manure. For1996 to 1997, the average seasonal CH₄emission for the double rice cropping periodwas the highest from the plot that was floodedin the winter (103.5 g CH₄ m^–2) andlowest from the plot planted and incorporatedwith Chinese milk vetch (32.6 gCH₄ m^–2). Precipitation in the winternot only affected growth of green manure, whichwas incorporated in situ, but might alsoaffect CH₄ emissions during the subsequentrice growing period. Therefore, a simplerelationship could not be found between theincorporated amount of green manure andCH₄ emission. In the plots incorporatedwith vetch and oil-seed rape straw CH₄emissions were significantly less during thesubsequent late-rice period than during theearly-rice period. This phenomenon might beattributed to a ``priming effect' of greenmanure, which exhausted soil labile organicmatter. Based on the CH₄ fluxmeasurements, the total CH₄ emissions fromrice fields in Hunan Province during the ricegrowing season were estimated as 1.56 TgCH₄ in 1996 and 1.06 Tg CH₄ in 1997.Large variation of precipitation in the winterwould be an important factor controlling theannual variation of CH₄ emissions from thetreatments.     

环境因子对植物释放挥发性化合物的影响

对近年来有关环境因子与植物释放挥发性化合物关系的研究进展进行了综合和概括。本文主要包括3类挥发性化合物。（1）异戊二烯是由叶绿体产生并且直接释放到大气中的C5化合物。（2）单萜类化合物是一类环状或非环状的C10化合物,它在植物体内合成后首先贮存于体内的特殊结构中（如树脂道、油腺）,然后由此通过气孔向大气中释放。（3）含氧挥发性化合物以各种形式释放到大气中。它包括醇、醛、酮、酯和有机酸。本文的重点是前两者, 主要阐述了二方面内容：(1)植物挥发性化合物的生物合成和释放机理。(2)环境因子（如温度、光照、水分胁迫、营养、CO2浓度、空气湿度）及植物的发育阶段、机械损伤和昆虫取食等对植物挥发性化合物合成与释放的影响机制。     

Characterization of a hypertriglyceridemic transgenic miniature pig model expressing human apolipoprotein CIII

Hypertriglyceridemia has recently been considered to be an independent risk factor for coronary heart disease, in which apolipoprotein (Apo)CIII is one of the major contributory factors, as it is strongly correlated with plasma triglyceride levels. Although ApoCIII transgenic mice have been generated as an animal model for the study of hypertriglyceridemia, the features of lipoprotein metabolism in mice differ greatly from those in humans. Because of the great similarity between pigs and humans with respect to lipid metabolism and cardiovascular physiology, we generated transgenic miniature pigs expressing human ApoCIII by the transfection of somatic cells combined with nuclear transfer. The expression of human ApoCIII was detected in the liver and intestine of the transgenic pigs. As compared with nontransgenic controls, transgenic pigs showed significantly increased plasma triglyceride levels (83 ± 36 versus 38 ± 4 mg·dL(-1), P < 0.01) when fed a chow diet. Plasma lipoprotein profiling by FPLC in transgenic animals showed a higher peak in large-particle fractions corresponding to very low-density lipoprotein/chylomicrons when triglyceride content in the fractions was assayed. There was not much difference in cholesterol content in FPLC fractions, although a large low-density lipoprotein peak was identified in both nontransgenic and transgenic animals, resembling that found in humans. Further analysis revealed markedly delayed clearance of plasma triglyceride, accompanied by significantly reduced lipoprotein lipase activity in post-heparin plasma, in transgenic pigs as compared with nontransgenic controls. In summary, we have successfully generated a novel hypertriglyceridemic ApoCIII transgenic miniature pig model that could be of great value for studies on hyperlipidemia in relation to atherosclerotic disorders.     

SAM domain-based protein oligomerization observed by live-cell fluorescence fluctuation spectroscopy

Sterile-alpha-motif (SAM) domains are common protein interaction motifs observed in organisms as diverse as yeast and human. They play a role in protein homo- and hetero-interactions in processes ranging from signal transduction to RNA binding. In addition, mutations in SAM domain and SAM-mediated oligomers have been linked to several diseases. To date, the observation of heterogeneous SAM-mediated oligomers in vivo has been elusive, which represents a common challenge in dissecting cellular biochemistry in live-cell systems. In this study, we report the oligomerization and binding stoichiometry of high-order, multi-component complexes of (SAM) domain proteins Ste11 and Ste50 in live yeast cells using fluorescence fluctuation methods. Fluorescence cross-correlation spectroscopy (FCCS) and 1-dimensional photon counting histogram (1dPCH) confirm the SAM-mediated interaction and oligomerization of Ste11 and Ste50. Two-dimensional PCH (2dPCH), with endogenously expressed proteins tagged with GFP or mCherry, uniquely indicates that Ste11 and Ste50 form a heterogeneous complex in the yeast cytosol comprised of a dimer of Ste11 and a monomer of Ste50. In addition, Ste50 also exists as a high order oligomer that does not interact with Ste11, and the size of this oligomer decreases in response to signals that activate the MAP kinase cascade. Surprisingly, a SAM domain mutant of Ste50 disrupted not only the Ste50 oligomers but also Ste11 dimerization. These results establish an in vivo model of Ste50 and Ste11 homo- and hetero-oligomerization and highlight the usefulness of 2dPCH for quantitative dissection of complex molecular interactions in genetic model organisms such as yeast.     

DHRS4L2非编码RNA调控CPNE6基因表达

DHRS4/NRDR基因编码一种属于SDR家族的酶,在维甲酸合成、类固醇代谢和苯甲基代谢中发挥生物合成催化作用.DHRS4基因定位于14q11-2,有两个相似的拷贝基因,分别为DHRS4L2和DHRS4L1.我们前期发现了DHRS4L2基因一个上游转录起始位点,命名为DHRS4L2-Ea.在本研究中,我们用RT-PCR和双脱氧测序法发现一个新的从DHRS4L2-Ea转录的选择性剪接亚型DHRS4L2-900a(KC237374).同时RT-PCR结果显示在SK-N-SH细胞DHRS4L2-Ea选择性剪接亚型中DHRS4L2 iso(AY616183)表达最多,为主要亚型.在SK-N-SH细胞过表达DHRS4L2-800a(AY920361)使DHRS4L2-Ea 基因下游CPNE6 mRNA表达下调.在HeLa细胞过表达DHRS4L2 800a(AY920361)或DHRS4L2-900a(KC237374) 进一步表明DHRS4L2 Ea抑制CPNE6表达的作用.定量PCR结果显示si-RNA抑制DHRS4L2-Ea表达使CPNE6 mRNA表达上调.亚硫酸盐测序结果显示在SK-N-SH转染DHRS4L2-800a(AY920361)的样本中CPNE6基因DNA CpG甲基化增加.综上所述,本研究揭示DHRS4L2表达的非编码RNA抑制其下游基因CPNE6的表达.     

Genotype and haplotype analysis of the AZGP1 gene in cattle

Zinc-a2-glycoprotien (AZGP1) involved in lipid metabolism and associated with adipose tissue atrophy in cachexia. And it also related to sperm motility and in turn fertilization. To ascertain whether there were mutations in the bovine AZGP1 gene, this study investigated variation of the AZGP1 gene through PCR-SSCP and sequencing. Four missense mutations were identified in 649 cattle from six independent populations. Haplotype frequencies and linkage disequilibrium (LD) coefficients of these SNPs in three Chinese indigenous cattle breeds were analyzed. One LD block was found in three cattle breeds. The statistical analyses indicated that AC genotype of Z4 locus was associated with the high body weight, body length and chest girth in Jiaxian cattle breed (P?<?0.05). Our results provided evidence that polymorphisms in the AZGP1 gene were associated with growth traits, and may be used for marker-assisted selection and management in cattle breeding program.     

Sequence Based Prediction of DNA-Binding Proteins Based on Hybrid Feature Selection Using Random Forest and Gaussian Na?ve Bayes

Developing an efficient method for determination of the DNA-binding proteins, due to their vital roles in gene regulation, is becoming highly desired since it would be invaluable to advance our understanding of protein functions. In this study, we proposed a new method for the prediction of the DNA-binding proteins, by performing the feature rank using random forest and the wrapper-based feature selection using forward best-first search strategy. The features comprise information from primary sequence, predicted secondary structure, predicted relative solvent accessibility, and position specific scoring matrix. The proposed method, called DBPPred, used Gaussian naïve Bayes as the underlying classifier since it outperformed five other classifiers, including decision tree, logistic regression, k-nearest neighbor, support vector machine with polynomial kernel, and support vector machine with radial basis function. As a result, the proposed DBPPred yields the highest average accuracy of 0.791 and average MCC of 0.583 according to the five-fold cross validation with ten runs on the training benchmark dataset PDB594. Subsequently, blind tests on the independent dataset PDB186 by the proposed model trained on the entire PDB594 dataset and by other five existing methods (including iDNA-Prot, DNA-Prot, DNAbinder, DNABIND and DBD-Threader) were performed, resulting in that the proposed DBPPred yielded the highest accuracy of 0.769, MCC of 0.538, and AUC of 0.790. The independent tests performed by the proposed DBPPred on completely a large non-DNA binding protein dataset and two RNA binding protein datasets also showed improved or comparable quality when compared with the relevant prediction methods. Moreover, we observed that majority of the selected features by the proposed method are statistically significantly different between the mean feature values of the DNA-binding and the non DNA-binding proteins. All of the experimental results indicate that the proposed DBPPred can be an alternative perspective predictor for large-scale determination of DNA-binding proteins.     

Gene cloning and functional analysis of yellow green leaf3 (ygl3) gene during the whole-plant growth stage in rice

Chlorophyll is an important photosynthetic pigment in the process of photosynthesis in plants and photosynthetic bacteria. Genes involved in chlorophyll biosynthesis in Arabidopsis and photosynthetic bacteria have been well documented. In rice, however, these genes have not been fully annotated. In this paper, a yellow-green leaf gene, yellow green leaf3 (ygl3) was cloned and analyzed. ygl3 encodes magnesium chelation ChlD (D) subunit, a key enzyme for chlorophyll synthesis, resulting in a yellow-green leaf phenotype in all growth stages in rice. Expression content of ygl3 is highest in the leaf blades, followed by the leaf sheaths, while there is virtually no expression of the gene in the stems and seeds. The sub-cellular structure and protein content of the photosynthetic system of the ygl3 mutant were revealed by transmission electron microscopy, BN-PAGE, and western blotting. The results show that the mutation of the ygl3 gene indirectly leads to a decrease in the protein content of the photosynthetic system and severely obstructs the formation of granum thylakoids.     

Characterization and molecular mapping of stripe rust resistance gene Yr61 in winter wheat cultivar Pindong 34

Key message

We report a new stripe rust resistance gene on chromosome 7AS in wheat and molecular markers useful for transferring it to other wheat genotypes.

Abstract

Several new races of the stripe rust pathogen have established throughout the wheat growing regions of China in recent years. These new races are virulent to most of the designated seedling resistance genes limiting the resistance sources. It is necessary to identify new genes for diversification and for pyramiding different resistance genes in order to achieve more durable resistance. We report here the identification of a new resistance gene, designated as Yr61, in Chinese wheat cultivar Pindong 34. A mapping population of 208 F₂ plants and 128 derived F_2:3 lines in a cross between Mingxian 169 and Pindong 34 was evaluated for seedling stripe rust response. A genetic map consisting of eight resistance gene analog polymorphism (RGAP), two sequence-tagged site (STS) and four simple sequence repeat (SSR) markers was constructed. Yr61 was located on the short arm of chromosome 7A and flanked by RGAP markers Xwgp5467 and Xwgp5765 about 1.9 and 3.9 cM in distance, which were successfully converted into STS markers STS5467 and STS5765b, respectively. The flanking STS markers could be used for marker-assisted selection of Yr61 in breeding programs.