Genotypes Analyses of Ten Genes Related to Eating Quality of Twenty-three Fragrant Rice Cultivars by Molecular Marker

Fragrance is a very important quality traits of rice, fragrant rice research has been an important research issue in rice research fields in nowadays. In our study, using the detection method of molecular markers, genotypes of the 10 genes (Wx, SSII 3, SBE3, AGPiso, SSIII 2, AGPlar, PUL, SSI, ISA, SSIV 2) associated rice eating quality were analyzed in the 23 fragrant rice cultivars. The result indicated that the “2845”rice cultivar possesses the best combination of genotypes related to the highest eating quality, and the next best rice cultivars were “Songxiangzaojing”, ”Suhuxiangjing”, “B1”, “Wuyun2645”, “Tongyunjing”, “Yinxiang28”, “Xiangjing49②”, “99983”, “Wxiang99075”, “07-08”, “Yunjingyou15”, “29185”, “Nanhai318”. Other 9 rice cultivars (“Dahuaxiangjing”, “Wuxiang14”, “Xiangjing”, “Della”, “Dalixiang”, “Taiguoxiangdao”, “Cxiang517”, “Xiangdao No1”, “Zhongxiang No1”) obtain some of bad genotypes which may have adverse effect on rice eating quality. This study was helpful to establish an overall understanding of the genotypes of these ten eating quality related genes in the 23 tested fragrant rice cultivars, and provides the important genotype information in selecting and cultivating new fragrant rice with good eating quality in future via molecular markers assisted selection method.     

P61 Protein from a Male Sterile Mutant of Rice is an Isoform of the Chloroplast ATPase β Subunit

P61 was a protein identified from chloroplasts of Nongken 58S, a male sterile mutant of rice (Oryza sativa L. ssp. japonica). Microsequence analysis has revealed that its N-terminal sequence was identical to N-termini of ATPase β subunits of chloroplasts from rice and barley. The antiserum produced using ATPase β subunit from maize specifically recognized P61. P61 had the same molecular weight as the chloroplast ATPase β subunit of wild-type rice “Nongken 58”, but had different isoelectric point (pI) from this β　subunit. P61 was more basic than this β subunit. Thus, P61 would be identified as an isoform of the chloroplast ATPase β subunit of rice, named β1. Genetic analysis with a F2 population of Nongken 58SדNongken 58” showed that a single recessive genic gene regulated the formation of β1.     

水稻耐光氧化和耐荫特性的生理基础

用简易、有效的人工光氧化和遮荫技术对30个水稻(Oryza sativa L.)种质进行筛选,鉴定出既耐光氧化又耐荫、耐光氧化不耐荫、耐荫不耐光氧化、既不耐荫又不耐光氧化等4种品种类型,并用既耐光氧化又耐荫的品种"武育粳3号"和对光氧化和遮荫均敏感的品种"香籼"进行光合特性研究.结果表明:在遮荫条件下,与对光氧化和遮荫敏感的品种"香籼"比较,"武育粳3号"的PSⅡ活性差异不大,RuBisCO活性降低较少,光合能力、光合生产力较高.在光抑制条件下,"武育粳3号"的PSⅡ活性,PSⅡ光化学效率(Fv/Fm),PSⅡ-D1蛋白含量降低较少,光合作用光抑制较轻.在光氧化条件下,内源活性氧清除剂SOD诱导活性高,清除O-能力强,因而叶绿素衰减较慢.上述研究为水稻育种提供了配套的优良生理特性的鉴定技术和生理依据.     

水稻基因APRT的克隆及其与温敏核雄性不育的关系

在拟南芥中腺嘌呤磷酸核糖转移酶基因(APRT)突变导致植株雄性不育.本文首次报道从水稻(Oryza sativa subsp.indica)中克隆了基因APRT(GenBank登录号AY238894),并将其定位于水稻第4染色体的一个BAC克隆(AL606604)的58 000 bp至63 000 bp区域.该基因长4 220 bp(起始密码子至终止密码子),含7个外显子、6个内含子,编码的APRT蛋白长212个氨基酸残基,与其他物种来源的APRT序列存在很高的同源性.与大麦、小麦、拟南芥1型及其2型的该蛋白同源性分别为54.9%、54.9%、49.6%和59.5%.经保守结构域搜索发现该蛋白中存在APRT催化结构域.从DNA、mRNA两个水平分析了该基因与水稻温敏核雄性不育(TGMS)的关系,结果表明:受温度诱导,水稻"安农S-1"APRT基因的表达变化可能与温敏核雄性不育表现型具相关性.     

Construction of EMS-Induced Peanut Mutant Libraries and Identification of Pod-Related Traits Mutant Lines

Peanut (Arachis hypogaea L.) is an oil and economic crop of vital importance, and peanut pod is the key organ influencing the yield and processing quality. Hence, the Pod-related traits (PRTs) are considered as important agronomic traits in peanut breeding. To broaden the variability of PRTs in current peanut germplasms, three elite peanut cultivars were used to construct Ethyl methane sulfonate (EMS)-induced mutant libraries in this study. The optimal EMS treatment conditions for the three peanut varieties were determined. It was found that the median lethal dose (LD50) of EMS treatment varied greatly among different genotypes. Finally, the EMS-induced peanut mutant libraries were constructed and a total of 124 mutant lines for PRTs were identified and evaluated. Furthermore, “M-8070”, one of the mutant lines for pod constriction, was re-sequenced via high-throughput sequencing technology. The genome-wide variations between “M-8070” and its wild parent “Fuhua 8” (FH 8) were detected. 2994 EMS-induced single nucleotide polymorphisms (SNPs) and 1188 insertion-deletions (InDels) between “M-8070” and its wild parent were identified. The predominant SNP mutation type was C/G to T/A transitions, while the predominant InDel mutation type was “1-bp”. We analyzed the distribution of identified mutations and annotated their functions. Most of the mutations (91.68% of the SNPs and 77.69% of the InDels) were located in the intergenic region. 72 SNPs were identified in the exonic region, leading to 27 synonymous, 43 non-synonymous and 2 stop-gain variation for gene structure. 13 Indels were identified in the exonic region, leading to 4 frame-shift, 8 non-frame-shift and 1 stop-gain variations of genes. These mutations may lead to the phenotypic variation of “M-8070”. Our study provided valuable resources for peanut improvement and functional genomic research.     

水稻的光合作用、生长、碳同位素分辨作用及抗渗透胁迫性对CO2浓度增高的响应

四个水稻(Oryza sativa L.)品种"IR72"、"特三矮2号"、"桂朝2号"和"Ⅱ优4480"在田间栽于含35 μmol/mol 和60 μmol/mol CO2的塑料大棚中,自然光照.高浓度CO2下供试水稻品种的光合速率变化表现为提高型("IR72"、"特三矮2号")、稳定型("桂朝2号"的Pn几无变化)和下调型("Ⅱ优4480").生长速率、穗重、由Δ13C计算而得的长期水分利用效率和清除DPPH@自由基的能力皆增加.除"Ⅱ优4480"外,其他3个品种明显增高总生物量.供试品种的穗重/总生物量比不同程度地受到高浓度CO2的改变.叶片段经PEG渗透胁迫后,不同的生长于高浓度CO2者的电解质渗漏率较小.结果表明高浓度CO2可改变水稻的光合作用和水分关系特性,品种间不同的响应显示了选育适于未来高浓度CO2下具有高产和抗逆性品种的可能性.     

Energy charge regulation in photosynthetic bacteria

The “energy charge” concept suggests that the relative concentrations of adenylate nucleotides in cellular pools define a signal system that is important in the regulation, and integration, of energy conversion and biosynthesis in growing cells. The results of experiments in which photosynthetic bacteria are subjected to treatments that could be expected to disturb the “normal” energy charge can be reasonably interpreted in terms of “energy charge control.”     

Comparative Spectroscopic Studies on the Photoinhibition Process in Photosystem ￠?Complex from Two Wheat Cultivars

The photodamage processes of PSⅠ particles isolated from two wheat cultivars “Jing 411” and “Xiaoyan 54” were studied by comparing the difference in spectroscopic properties. It was found that high light intensity caused the damage of pigments in PSⅠ, especially Chl a molecules with maximum absorption at 683 nm is very sensitive to high light. The change in fluorescence spectra revealed that photodamage also led to the damage of the process of energy transfer in PSⅠ. In the PSⅠ particles “Xiaoyan 54”, the absorption of Chl a molecules at 683 nm slightly decreased at the beginning of illumination and meanwhile the fluorescence become stronger, but the absorption become stable rather long, and declining after 40 min. On the other hand, PSⅠ particles of “Jing 411” showed no such changes during the process of photodamage. Presumably in PSⅠ of “Xiaoyan 54”, excessive energy was distributed to long wave chlorophyll molecules and the number of antenna pigment molecules was less, so that less energy was transferred to the reaction center P700 and thus it was protected. This is the possible reason why “Xiaoyan 54” was more resistant to photooxidation.     

Quasi-species evolution in subdivided populations favours maximally deleterious mutations

Most models of quasi-species evolution predict that populations will evolve to occupy areas of sequence space with the greatest concentration of neutral sequences, thus minimizing the deleterious mutation rate and creating mutationally 'robust' genomes. In contrast, empirical studies of the principal model of quasi-species evolution, RNA viruses, suggest that the effects of deleterious mutations are more severe than in similar DNA-based microbes. We demonstrate that populations divided into discrete patches connected by dispersal may favour genotypes where the deleterious effect of non-neutral mutations is maximized. This effect is especially strong in the absence of back mutation and when the amount of time spent in hosts prior to dispersal is intermediate. Our results indicate that RNA viruses that produce acute infections initiated by a small number of virions are expected to evolve fragile genetic architectures when compared with other RNA viruses.     

The standard genetic code enhances adaptive evolution of proteins

The standard genetic code, by which most organisms translate genetic material into protein metabolism, is non-randomly organized. The Error Minimization hypothesis interprets this non-randomness as an adaptation, proposing that natural selection produced a pattern of codon assignments that buffers genomes against the impact of mutations. Indeed, on the average any given point mutation has a lesser effect on the chemical properties of the utilized amino acid than expected by chance. Might it also, however, be the case that the non-random nature of the code effects the rate of adaptive evolution? To investigate this, here we develop population genetic simulations to test the rate of adaptive gene evolution under different genetic codes. We identify two independent properties of a genetic code that profoundly influence the speed of adaptive evolution. Noting that the standard genetic code exhibits both, we offer a new insight into the effects of the "error minimizing" code: such a code enhances the efficacy of adaptive sequence evolution.     

长链非编码RNA研究进展

基因组计划研究表明, 在组成人类基因组的30亿个碱基对中, 仅有1.5%的核酸序列用于蛋白质编码, 其余98.5%的基因组为非蛋白质编码序列。这些序列曾被认为是在进化过程中累积的“垃圾序列”而未予以关注, 但在随后启动的ENCODE研究计划中却发现, 75%的基因组序列能够被转录成RNA, 其中近74%的转录产物为非编码RNA(Non-coding RNA, ncRNA)。在非编码RNA中, 绝大多数转录本的长度大于200个碱基, 这些“长链非编码RNA(Long non-coding RNA, lncRNA)”能够在转录及转录后水平上调节蛋白编码基因的表达, 从而广泛地参与包括细胞分化、个体发育在内的重要生命过程, 其异常表达还与多种人类重大疾病的发生密切相关。文章综述了长链非编码RNA的发现、分类、表达、作用机制以及其在个体发育和人类疾病中的作用。     

Effect of Heat Stress on Photosynthetic Characteristics of Different Green Organs of Winter Wheat During Grain-filling Stage

Four winter wheat ( Triticum aestivum L.) varieties (“JD 8”, “Jing 411”,“Centurk” and “Tam 202”) were used to study the effect of heat stress on photosynthetic characteristics of flag leaf blade, flag leaf sheath, peduncle, glume, lemma and awn during grain-filling stage. The results showed that heat acclimation during grain-filling stage increased thermotolerance of wheat with significant differences among different green organs. During heat stress, the decreases of the efficiency of primary light energy conversion ( Fv/Fm ) of PS and pigment (chlorophyll and carotenoid) content were much slower in peduncle, flag leaf sheath and glume than in flag leaf blade, lemma and awn; and the percentage of decrease in net photosynthetic rate ( Pn ) of ear was lower than that of the flag leaf blade. The measured photosynthetic parameters ( Fv/Fm , Pn and pigment content) of “JD 8”, a relatively heat tolerant variety, declined more slowly than those of the other three varieties during the whole heat stress period.      

Measurement of 131 I and 125 I by liquid scintillation counting

When aqueous samples are made miscible with a toluene scintillation solution by means of Bio-Solv BBS-3, high ¹²⁵I and ¹³¹I efficiencies can be achieved over a considerable range of “impurity” quenching, and adequate isotope separations can be achieved using liquid scintillation counters with “linear,” “pseudologarithmic,” or “logarithmic” amplification. Using an example of each sort of counter, we have graphically outlined the two somewhat different procedures for choosing the best instrument settings for single- and double-isotope counting. “Linear” instruments, despite a slightly more complex procedure for selection of settings, may offer the advantage, in double-isotope counting, of somewhat greater isotope separations because of the greater attenuation of photo-electron spectra.     

钼、硼对大豆叶片膜脂过氧化及体内保护系统的影响

The study deals with the changes of membrane peroxidation and endogenous protective system with different supplementation of molybdenum (Mo) and/or boron (B) concentration in soybean (Glycine max L.) leaves at three developmental stages (5-trifoliate stage, initiation of flowering, and peak podsetting stage) in three pot-grown soybean varieties (“Zhechun No.3”, “Zhechun No.2”, “3811”). The control plants under low Mo and low B exhibited an increasing of membrane permeability (MP), malondialdehyde (MDA) and proline (Pro) contents, polyphenol oxidase (PPO) and ascorbate oxidase (AO) activities and a decrease of ascorbate (AsA) contents, superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (AP) and catalase (CAT) activities. Application of Mo or B alone raised the ability of anti-oxidant of soybean leaves. The results indicated that the anti-oxidant enzymes (including SOD, POD, CAT and AP) related closely to anti-oxidant compounds (including AsA and Pro). There was some difference between the effects of Mo and B on the anti-oxidant, and a synergetic effect was observed between Mo and B. Some genetic variation in the responses to Mo and B was found among the three soybean varieties which was related to the activities of the total anti-oxidant systems.     

Intra-host genetic heterogeneity of hepatitis C virus and biomedical implications

The HCV genome exhibits significant intra-host genetic heterogeneity as the result of accumulation of mutations during viral replication. At each point in time during the infection, the viral population is composed of a dominant master sequence and a number of sequences diverging from the master sequence to various extents (the viral quasi-species). The quasispecies is a complex, dynamic distribution of nonidentical, but related, replicons. In these populations, viral variants may undergo very large changes in their fitness (the replicative adaptability of an organism to its environment), including dramatic fitness loss and important fitness gains. The biological impact of this event may theoretically include modifications of tropism, appearance of escape mutants, changes in pathogenic potential, and resistance to antiviral agents. A growing body of molecular and clinical data currently suggests that both inter- and intra-host genetic heterogeneity of HCV have crucial biological and medical implications, influencing not only infection prevention, but also clinical progression of chronic liver disease in persistently infected subjects, HCV infection of non-liver cells, and response to the anti-viral therapy.     

C4 Pathway Enzymes in Soybean Leaves

High-yielding soybean ( Glycine max (L.) Merr.) variety, “Heinong 40”, and one control variety, “Heinong 37”, were used as experimental materials. The activities of C4 pathway enzymes, i.e. PEPCase (phosphoenolpyruvate carboxylase), NADP-ME (NADP-malic enzyme), NADP-MDH (NADP-malate dehydrogenase), PPDK (pyruvate phosphate dikinase) and RuBPCase (ribulose-1.5-bisphosphate carbozylase) were assayed at seedling, blooming, pod-bearing and pod-filling stage. The results indicated that C4 pathway enzymes were expressed differently at different developing stages in both varieties of soybean, but the ratio of PEPCase and RuBPCase showed that the expression of C4 pathway enzymes of “Heinong 40” was higher than those of “Heinong 37” at each stage. The results showed that C4 pathway enzymes were closely related to the crop yielding potential. Therefore, it is possible to select potentially high-yielding soybean variety by the expression of C4 pathway enzymes.     

雪花莲外源凝集素基因转化番茄

The plasmid pRSSGNA1 carried a snowdrop lectin gene (Galanthus nivalis agglutinin, GNA) under the drive of RSs-1 promoter, were successfully transferred into three tomato (Lycopersicon esculentum Mill.) cultivars, “C8”,“A39” and “A53” via Agrobacterium-mediated transformation. Regenerated plantlets were obtained from cotyledons after preculture, shoot inducing culture and root inducing culture. Transgenic tomato plants were confirmed by the kanamycin-resistant experiment, PCR analysis and Southern blot. The preliminary results from bioassay demonstrated significant resistance of the transgenic plants to aphid (Myzus persicae Sulzer) larvae. The inheritance of selective marker gene (NPTⅡ) in 3 transgenic tomato plants is in the model of the simple Mendel's fashion in progenies of the selfing generation.     

Proceedings of the international workshop on Ribosomal RNA technology, April 7-9, 2008, Bremen, Germany

Thirty years have passed since Carl Woese proposed three primary domains of life based on the phylogenetic analysis of ribosomal RNA (rRNA) genes. Adopted by researchers worldwide, rRNA has become the “gold-standard” for molecular taxonomy, biodiversity analysis and the identification of microorganisms. The more than 700,000 rRNA sequences in public databases constitute an unprecedented hallmark of the richness of microbial biodiversity on earth. The International Workshop on Ribosomal RNA Technology convened on April 7–9, 2008 in Bremen, Germany (http://www.arb-silva.de/rrna-workshop) to summarize the current status of the field and strategize on the best ways of proceeding on both biological and technological fronts. In five sessions, 26 leading international speakers and ∼120 participants representing diverse disciplines discussed new technological approaches to address three basic ecological questions: “Who is out there?” “How many are there?” and “What are they doing?”.     

Studies on a Gynoecious-specific ACC Synthase Gene in Different Sexual Phenotypes of Cucumber Genome

Using a pair of primers (Primer Ⅰ and Primer Ⅱ), the authors have amplified a fragment of ACC synthase gene about 1025 bp from four varieties of gynoecious species of cucumber （Cucumis sativus L.） viz.:“CORONA”,“DALEVE”,“Zhongnong No.5”,and “Ouzhou No.8”. Sequence analysis revealed that this fragment of ACC synthase gene was more than 99% homologous with the gene reported by Trebitsh et al (1997). The authors regard them as the same gene, but it exhibited less homology with this ACC synthase gene when expressed by other induction. Southern blot analysis showed that this fragment of ACC synthase gene is associated with the sexual phenotype of cucumber,and it is the specific gene of gynoecium. However, the number of its copies has no direct correlation with the degree of female expression; this seems to indicate that there might be other genes associated with the degree of feminization.     

Arbitrariness is not enough: towards a functional approach to the genetic code

Arbitrariness in the genetic code is one of the main reasons for a linguistic approach to molecular biology: the genetic code is usually understood as an arbitrary relation between amino acids and nucleobases. However, from a semiotic point of view, arbitrariness should not be the only condition for definition of a code, consequently it is not completely correct to talk about “code” in this case. Yet we suppose that there exist a code in the process of protein synthesis, but on a higher level than the nucleic bases chains. Semiotically, a code should be always associated with a function and we propose to define the genetic code not only relationally (in basis of relation between nucleobases and amino acids) but also in terms of function (function of a protein as meaning of the code). Even if the functional definition of meaning in the genetic code has been discussed in the field of biosemiotics, its further implications have not been considered. In fact, if the function of a protein represents the meaning of the genetic code (the sign’s object), then it is crucial to reconsider the notion of its expression (the sign) as well. In our contribution, we will show that the actual model of the genetic code is not the only possible and we will propose a more appropriate model from a semiotic point of view.