基于比较基因组学方法的丝状子囊菌同源序列分析

为探讨丝状子囊菌基因组的同源保守序列作为标记基因,利用Standalone BLASTN方法将构巢曲霉全基因组基因分别与30种丝状子囊菌基因组比较.构巢曲霉与每个丝状子囊菌基因组之间的同源匹配基因数量似乎可反映子囊菌之间的进化关系,构巢曲霉（10,560个基因）与15种散囊菌纲其他真菌间的匹配基因数量为5,179-7,747个,其中与另外7个同属的种匹配的基因数量为7,434-7,747个,而与亲缘关系较远的2种锤舌菌纲真菌灰葡萄孢和核盘菌的匹配基因数量分别仅有4,318个和4,242个.构巢曲霉的10,560个基因与20余种子囊菌基因组同时匹配的基因数为3,509个,占33.2％,构巢曲霉基因与30种子囊菌共同匹配的基因仅924个.此外,E值大小在10-30_0.1范围的同源序列变异性大,而在0-10-100范围的同源序列高度保守.随着基因组序列数据的增加,比较基因组方法将会在真菌系统学研究领域发挥更大的作用.     

Lung injury risk assessment during blast exposure

Blast pulmonary trauma are common consequences of modern war and terrorism action. To better protect soldiers from that threat, the injury risk level when protected and unprotected must be assessed. Knowing from the literature that a possible amplification of the blast threat would be provided by some thoracic protective systems, the objective is to propose an original approach to correlate a measurable parameter on a manikin with a pulmonary risk level. Using a manikin whose response is correlated with the proposed tolerance limits should help in the evaluation of thoracic protective system regarding injury outcomes.A database including lung injury data from large mammals have been created, allowing the definition of iso-impulse tolerance limits from no lung injury to severe ones (∼60% of ecchymosis). As the use of this metric is not sufficient to evaluate the performance of protective systems on a manikin, the iso-impulse tolerance limits were associated with the thoracic response of post-mortem swine under blast loading. It was found that the lung injury threshold in terms of incident impulse is 58.3 kPa·ms, corresponding to a chest wall peak of acceleration/velocity/displacement of 7350 m/s², 3.7 m/s and 6.4 mm respectively. Lung injuries are considered as severe (30–60% of ecchymosis) when the incident impulse exceed 232.8 kPa·ms, leading to a chest wall peak of acceleration/velocity/displacement of 79.7 km/s², 14.7 m/s and 30.1 mm respectively.The defined lung tolerance limits are valid for a 50 kg swine (unprotected) exposed side-on to the blast threat and against a wall.     

Molecular mapping of genes for resistance to rice blast (Pyricularia grisea Sacc.)

Two dominant genes conferring complete resistance to specific isolates of the rice blast fungus, Pyricularia grisea Sacc., were located on the molecular map of rice in this study. Pi-l(t) is a blast resistance gene derived from the cultivar LAC23. Its map location was determined using a pair of nearly isogenic lines (NILs) and a B₆F₃ segregating population from which the isoline was derived. RFLP analysis showed that Pi-l(t) is located near the end of chromosome 11, linked to RZ536 at a distance of 14.0±4.5 centiMorgans (cM). A second gene, derived from the cultivar Apura, was mapped using a rice doubled-haploid (DH) population. This gene was located on chromosome 12, flanked by RG457 and RG869, at a distance of 13.5+-4.3 cM and 17.7+-4.5 cM, respectively. The newly mapped gene on chromosome 12 may be allelic or closely linked toPi-ta. (=Pi-4(t)), a gene derived from Tetep that was previously reported to be linked to RG869 at a distance of 15.4±4.7 cM. The usefulness of markers linked to blast resistance genes will be discussed in the context of breeding for durable blast resistance.     

Saturation mapping with subclones of YACs: DNA marker production targeting the rice blast disease resistance gene, Pi-b

Saturation mapping of a very small genomic region is indispensable for map-based cloning. We applied a method based on sub-cloning and the Southern-hybridization technique for generating RFLP markers directly from yeast artificial chromosomes (YACs). Two YACs overlapping each other and covering the locus of the rice blast resistance gene, Pi-b, were used to construct a plasmid sub-library. Rice-specific and single-copy clones suitable as probes for RFLP analysis were selected from this sub-library by hybridization to the blots of digested DNAs of rice, YACs, and yeast. As a result, 22 markers were produced within a small chromosomal region including Pi-b. This case study shows that overlapping YACs known to cover the gene of interest are very useful in fine-scale physical mapping leading to map-based cloning of the target gene. Received: 2 May 1996 / Accepted: 2 August 1996     

Quantitative characterization of animal behavior following blast exposure

The simplest approach to quantifying animal behavior begins by identifying a list of discrete behaviors and observing the animal’s behavior at regular intervals for a specified period of time. The behavioral distribution (the fraction of observations corresponding to each behavior) is then determined. This is an incomplete characterization of behavior, and in some instances, mild injury is not reflected by statistically significant changes in the distribution even though a human observer can confidently and correctly assert that the animal is not behaving normally. In these circumstances, an examination of the sequential structure of the animal’s behavior may, however, show significant alteration. This contribution describes procedures derived from symbolic dynamics for quantifying the sequential structure of animal behavior. Normalization procedures for complexity estimates are presented, and the limitations of complexity measures are discussed.     

龟裂链霉菌中zwf基因的克隆及其生物信息学分析

利用RT-PCR技术、巢式PCR技术、3′-RACE和5′-RACE技术从龟裂链霉菌K-16菌株中克隆获得zwf基因的全长cDNA序列。测序结果表明：经软件Vector NTI 11.0拼接zwf基因全长cDNA序列为1 679 bp,并带有一段很短的poly(A)尾巴,包含1 347 bp的开放读码框(ORF),编码一个含449个氨基酸残基的蛋白质。Blast2go生物信息学分析结果表明：该基因编码的酶为葡萄糖-6-磷酸脱氢酶,通过KEGG代谢途径注释明确该基因编码的酶是参与谷胱甘肽代谢和磷酸戊糖途径代谢的关键酶。     

CO2 reduction potentials by utilizing waste plastics in steel works

Background, aim, and scope  Feedstock recycling has received attention as an effective method to recycle waste plastics. However, estimating the reduction potential by life cycle assessment using coke oven and blast furnace in steel works has been a challenging task due to the complex structure of energy flow in steel works. Municipal waste plastics consist of several plastic resins. Previous studies have generally disregarded the composition of waste plastics, which varies significantly depending on the geographical area. If the reduction potentials by using each plastic resin in steel works can be quantified, the potential of municipal waste plastics (mixtures of plastic resins) can be estimated by summing up the potential of each resin multiplied by the composition of each resin in municipal waste plastics. Therefore, the goal of this study is to investigate the reduction potentials of CO₂ emissions by using individual plastic resins (polyethylene (PE), polypropylene (PP), polystyrene (PS), polyethylene terephthalate (PET)) and those for municipal waste plastics in the coke oven and blast furnace. Materials and methods  A model was developed to clarify the energy flow in steel works. In order to estimate the changes in energy and material balance in coke ovens when waste plastics are charged, the equations to calculate the coke product yield, gas product yield, and oil product yields of each plastic resin were derived from previous studies. The Rist model was adopted to quantify the changes in the inputs and outputs when plastics were fed into a blast furnace. Then, a matrix calculation method was used to calculate the change in energy balance before and after plastics are fed into a coke oven. Results  It was confirmed that product yields of municipal waste plastics (mixtures of plastic resins) could be estimated by summing up the product yield of each plastic resin multiplied by the composition of each resin in municipal waste plastics. In both cases of coke oven and blast furnace feedstock recycling, the reduction potential of CO₂ emissions varies significantly depending on the plastic resins. For example, in the case of coke oven chemical feedstock recycling, the reduction potential of PS and PP is larger than that of PE. On the other hand, in the case of blast furnace feedstock recycling, PE has the largest CO₂ emissions reduction potential, whereas the CO₂ emission reduction potential of PP is smaller than those of PE and PS. In both cases, PET has negative CO₂ emission reduction potentials, i.e., there is an increase of CO₂ emissions. In addition, the reduction potentials of CO₂ emissions are slightly different in each city. Discussions  The differences in the reduction potentials of CO₂ emissions by coke oven chemical feedstock recycling of each plastic resin is attributable to the differences in calorific values and coke product yields of each plastic resin. On the other hand, the difference in the CO₂ emission reduction potential for each plastic resin in blast furnace feedstock recycling is attributable to the difference in calorific values and the carbon and hydrogen content of each plastic resin, which leads to a difference in the coke substitution effect by each plastic resin. In both cases, the difference in those of municipal waste plastics is mostly attributable to the amount of impurities (e.g., ash, water) in the municipal waste plastics. Conclusions  It was found that the reduction potential of CO₂ emissions by coke oven and blast furnace feedstock recycling of municipal waste plastics (mixtures of plastic resins) could be estimated by summing up the potential of each resin multiplied by the composition of each resin in municipal waste plastics. It was also clarified that feedstock recycling of waste plastic in steel works is effective for avoiding the increase in CO₂ emissions by incinerating waste plastics, such as those from household mixtures of different resins. Recommendations and perspectives  With the results obtained in this study, reduction potentials of CO₂ emissions can be calculated for any waste plastics because differences in composition are taken into account.     

水稻品种矮梅早3号抗稻瘟病的遗传

水稻杂交组合(矮梅早3号×华矮837)的F_3株系接种菌株78-189(ZD_3)和83-182(ZD_1),应用累积分布曲线法进行了抗稻瘟遗传分析,结果表明:水稻品种矮梅早3号含有4个主效抗性基因P_i-A_1、P_i-A_2、P_i-A_3和P_i-A_4,其中P_i-a_4为隐性基因。P_i-A_1和P_i-A_2控制对菌株78-189(ZD_3)的高抗性,同时,P_i-A_2兼控M类型对菌株78-189(ZD_3)的抗性。P_i-A_3,控制对菌株83-182(ZD_1)的抗性。P_i-A_4控制M类型对菌株83-182(ZD_1)的抗性。水稻品种华矮837对以上两菌株不存在抗性基因。     

Improving the quality of twilight-zone alignments

Several recent publications illustrated advantages of using sequence profiles in recognizing distant homologies between proteins. At the same time, the practical usefulness of distant homology recognition depends not only on the sensitivity of the algorithm, but also on the quality of the alignment between a prediction target and the template from the database of known proteins. Here, we study this question for several supersensitive protein algorithms that were previously compared in their recognition sensitivity (Rychlewski et al., 2000). A database of protein pairs with similar structures, but low sequence similarity is used to rate the alignments obtained with several different methods, which included sequence-sequence, sequence-profile, and profile-profile alignment methods. We show that incorporation of evolutionary information encoded in sequence profiles into alignment calculation methods significantly increases the alignment accuracy, bringing them closer to the alignments obtained from structure comparison. In general, alignment quality is correlated with recognition and alignment score significance. For every alignment method, alignments with statistically significant scores correlate with both correct structural templates and good quality alignments. At the same time, average alignment lengths differ in various methods, making the comparison between them difficult. For instance, the alignments obtained by FFAS, the profile-profile alignment algorithm developed in our group are always longer that the alignments obtained with the PSI-BLAST algorithms. To address this problem, we develop methods to truncate or extend alignments to cover a specified percentage of protein lengths. In most cases, the elongation of the alignment by profile-profile methods is reasonable, adding fragments of similar structure. The examples of erroneous alignment are examined and it is shown that they can be identified based on the model quality.