Analysis of substitution events in HIV-1 vif gene of the Korean clade

Nucleotide and amino acid substitution pattern in vif gene of the Korean clade of HIV-1 isolated from Koreans were analyzed using consensus sequences. At nucleotide level, transition/transversion substitution ratio was 1.88, and nonsynonymous/synonymous substitution ratio was 2.67, suggesting a divergent evolution in the Korean clade. At amino acid level, there were 17 substitutions and G-->E substitution at position 37 may be responsible for change in predicted secondary structure.     

不同硫取代度昆布多糖硫酸酯的合成及理化性质初步研究

目的:对昆布多糖进行不同硫取代度的硫酸酯化修饰,并对其产物的硫酸基含量、糖含量与分子量进行检测,为研究不同硫取代度昆布多糖硫酸酯的生物活性奠定物质基础。方法:采用氯磺酸-吡啶法对昆布多糖进行硫酸化修饰,通过改变硫酸化修饰条件,来制取不同硫酸基取代度的昆布多糖硫酸酯;利用盐酸水解-硫酸钡比浊法测定昆布多糖硫酸酯的硫酸基含量,并通过公式求得其硫取代度;用苯酚-硫酸法测定昆布多糖硫酸酯的多糖含量,并使用HPGPC法测定其分子量。结果:两种不同硫取代度昆布多糖硫酸酯的硫酸基含量分别为37.8%、45.92%,取代度分别为1.07、1.51,糖含量分别为44.52%、37.19%,分子量分别为13000、16000。结论:利用氯磺酸-吡啶法对昆布多糖进行硫酸酯化修饰,该方法可以获取不同取代度产物,酯化率高。     

农业化学投入强度替代效率及其影响因素

采用SE-DEA和空间基尼系数,研究了2000—2016年我国农业化学投入强度替代效率,并运用Tobit模型分析了我国及各地区替代效率的驱动因素.结果表明: 我国农业化学投入强度替代的综合效率和规模效率呈现出“N”字型趋势,纯技术效率则波动上升,替代效率的地区差异明显,东部地区更倚重替代要素的投入规模;各年份全国省域差异最高的是综合效率,其次为纯技术效率,规模效率的区域差异性最小,地区内部省域差异逐渐减小,东部地区省域差异最大;农业化学投入替代效率受农业技术水平、农户收入水平、农业生产结构、农业发展程度和工业化水平的显著影响,各地区受各因素影响差异明显.推动农业化学投入替代效率,要从提高农业化学投入强度替代要素的投入效率、调整农用工业发展结构、关注农民收入水平和修订农业化学投入强度替代的补贴政策等方面入手.     

澜沧江梯级开发下鱼类支流生境替代效果

作为干流高坝水电开发导致鱼类生境丧失的一种补偿措施,支流替代生境近年来被广泛应用于受工程影响河段的土著鱼类保护,但替代支流发挥怎样的保护效果及干流对其的影响仍不清楚。以实施了澜沧江梯级生境替代的支流基独河与罗梭江为研究对象,并选择了邻近的对照支流,通过对鱼类调查数据的分析对比,揭示了各支流鱼类种类组成与群落结构的差异特征,初步阐明了梯级开发下鱼类支流生境替代效果以及干流工程建设对其的影响。结果表明：澜沧江支流替代生境对干流鱼类具有明显的保护作用,支流生境修复后鱼类物种丰富度明显提高,罗梭江土著鱼类、特有鱼类物种数分别增加了12种、7种,基独河则是7种、2种,替代生境能为澜沧江土著鱼类、部分濒危特有鱼类和洄游鱼类提供完成生活史的关键栖息地。干流对支流生境替代保护有着重要影响,罗梭江、基独河与邻近干流鱼类群落的Bray-Curtis相似性分别为21.76%、10.73%,支流河口段保持“河相”是支流生境替代保护效果可持续的关键。综合考虑生境替代保护的效益与投入,建议今后开展此类保护措施时优先选择库尾河相区的支流。     

Dipeptide backbone conformation and antibody recognition of a viral octapeptide epitope.

The peptide YKGTMDSG (Tyr-Lys-Gly-Thr-Met-Asp-Ser-Gly) represents an important antigenic determinant from the glycoprotein G2 of the pathogenic Rift Valley fever virus. By preparing a series of single-residue substitution peptides, the importance to antigenicity of individual residues within this octapeptide has been determined. Here, we investigated a simple and rapid computational analysis to test for correlations between the observed antigenicity of the substitution analogue peptides and the calculated conformational preferences in local regions of the peptides. Conformational energy analyses were carried out on all dipeptide combinations represented in the wild-type octapeptide and in the single-residue substitution analogue peptides. Conformational similarities and differences between wild-type and substitution dipeptide pairs were determined. The results of these computational analyses were then compared with the data on the relative antigenicity of the wild-type octapeptide and the substitution analogues. This comparison revealed a positive correlation. Substitution peptides showing changes in antigenicity possessed significant changes in the calculated backbone conformation relative to wild type in the dipeptides encompassing the residue substitution. Substitution peptides showing no change in antigenicity similarly showed no significant changes in dipeptide conformation. The potential utility of dipeptide conformational energy analyses and this preliminary structure-activity correlation are discussed.     

Rates of Synonymous Substitution and Base Composition of Nuclear Genes in Drosophila

We compared the rates of synonymous (silent) substitution among various genes in a number of species of Drosophila. First, we found that even for a particular gene, the rate of synonymous substitution varied considerably with Drosophila lineages. Second, we showed a large variation in synonymous substitution rates among nuclear genes in Drosophila. These rates of synonymous substitution were correlated negatively with C content and positively with A content at the third codon positions. Nucleotide sequences were also compared between pseudogenes and their functional homologs. The C content of the pseudogenes was lower than that of the functional genes and the A content of the former was higher than that of the latter. Because the synonymous substitution for functional genes and the nucleotide substitution for pseudogenes are exempted from any selective constraint at the protein level, these observations could be explained by a biased pattern of mutation in the Drosophila nuclear genome. Such a bias in the mutation pattern may affect the molecular clock (local clock) of each nuclear gene of each species. Finally, we obtained the average rates of synonymous substitution for three gene groups in Drosophila; 11.0 x 10(-9), 17.5 x 10(-9) and 27.1 x 10(-9)/site/year.     

Nucleophilic substitution at the anomeric position of 1,2-O-isopropylidenefuranose derivatives. A novel stereoselective synthesis of cyclic phosphates analogous to cAMP

1,2-O-Isopropylidenefuranose derivatives were treated with various nucleophiles in the presence of either BF(3).OEt(2) or trimethylsilyl trifluoromethanesulfonate (TMSOTf) leading to substitution products in a regio- and stereoselective manner. In particular, nucleophilic substitution of 1,2-O-isopropylidenefuranose derivatives when treated with allyltrimethylsilane was controlled by steric and electronic factors (similar to Woerpel's stereoelectronic model). On the other hand, when 1,2-O-isopropylidenefuranose derivatives were treated with trimethylsilane, in the presence of bis-O-trimethylsilyl-5-iodouracil or bis-O-trimethylsilyl-thymidine, substitution products were generated in high regio- and stereoselectivities via an unusual nucleophilic substitution with opening of the furanose ring. Based on these results, a stereoselective method for the synthesis of neutral cyclic phosphates analogous to cAMP was developed.     

Transformation of Azo Dye Isomers by Streptomyces chromofuscus A11

Fourteen mono-azo dyes were used to study the effects of substitution patterns on the biodegradability of dimethyl-hydroxy-azobenzene 4(prm1)-sulfonic acids by Streptomyces chromofuscus A11. Two substitution patterns were analyzed: (i) all possible substitution patterns of the two methyl and hydroxy substitution groups, 2-hydroxy (3,5; 4,5; 5,6) dimethyl and 4-hydroxy (2,3; 2,5; 2,6; 3,5) dimethyl isomers of azobenzene 4(prm1)-sulfonic acid; and (ii) replacement of the sulfonic group with a carboxylic group in these sulfonated azo dyes. The structural pattern of the hydroxy group in para position relative to the azo linkage and of two methyl substitution groups in ortho position relative to the hydroxy group was the most susceptible to degradation. Replacement of the sulfonic group with a carboxylic group enhanced overall dye degradability by S. chromofuscus A11.     

Localization of glycosaminoglycan substitution sites on domain V of mouse perlecan

Perlecan, the predominant basement membrane proteoglycan, has previously been shown to contain glycosaminoglycans attached at serine residues, numbers 65, 71, and 76, in domain I. However, the C-terminal domains IV and V of this molecule may also be substituted with glycosaminoglycan chains, but the exact substitution sites were not identified. The amino acid sequence of mouse perlecan reveals many ser-gly sequences in these domains that are possible sites for glycosaminoglycan substitution. We expressed recombinant domain IV and/or V of mouse perlecan in COS-7 cells and analyzed glycosaminoglycan substitution. Both heparan sulfate and chondroitin sulfate chains could be detected on recombinant domain V. One site, ser-gly-glu (serine residue 3593), toward the C-terminal region of domain V is a substitution site for heparan sulfate. When this sequence was absent, chondroitin/dermatan sulfate substitution was deleted, and the likely site for this galactosaminoglycan substitution was ser-gly-ala-gly (serine residue 3250) on domain V.     

普通小麦-华山新麦草异代换系的分子细胞遗传学研究

利用荧光原位杂交和染色体 C-分带技术对普通小麦 -华山新麦草的异代换系进行了研究 .荧光原位杂交结果显示 :异代换系 H92 1- 6 - 12和 H92 4 - 3- 4均含有 2条华山新麦草的染色体 .对这 2个材料和华山新麦草进行染色体 C-分带带型比较 ,结果认为 :H92 1- 6 - 12可能是普通小麦 -华山新麦草的 5 A / N5h 代换系 ,H92 4 - 3- 4可能是 3D/ N4 h代换系 .     

The effect of selection for phenotypical characters on the chromosome constitution in spring triticale

A set of spring triticale selection forms was studied with the use of microsatellite markers specific for D-genome chromosomes and genomic in situ hybridization. 2R/2D substitutions were found in six of twelve forms. Two lines displayed segregation for the substitution: plants with the substitution and without it, and plants heterozygous for the substitution were revealed. Segregation of the lines and the presence in them of telocentric chromosomes of wheat and rye in the monosomic state suggest that the process of formation is still in progress. The data obtained also demonstrate that triticale is under selection for the 2R/2D substitution as controlling the spectrum of adaptively and selectively valuable traits.     

百合目叶绿体rbcL基因核苷酸替代速率检测

分析了百合目主要类群叶绿体中编码核酮糖1,5二磷酸羧化氧化酶大亚基rbcL基因的42条序列,使用RRTree相对速率检测方法,详细研究rbcL基因在百合目7科间同义替代速率和非同义替代速率的变化.相对速率检测显示:百合目内秋水仙科(Colchicaceae)的同义替代速率和非同义替代速率均最快,金梅草科(Campynemat-aceae)同义替代速率最慢,百合科(Liliaceae)的非同义替代速率最慢,但在百合目各科间,无论同义替代速率还是非同义替代速率差异均不显著.     

Effect of individual Sumai 3 chromosomes on resistance to scab spread within spikes and deoxynivalenol accumulation within kernels in wheat

Two sets of substitution lines were developed by crossing individual monosomic lines of Chinese Spring (recipient) with scab (Fusarium graminearum) resistant cultivar Sumai 3 (donor) and then using the monosomics as the recurrent male parent for four backcrosses (without selfing after each backcross). The disomic substitution lines were separated from selfed BC4F2 plants. Chromosome specific SSR markers were analyzed for polymorphism between Sumai 3 and Chinese Spring. Polymorphic markers were used to identify substitution lines for specific chromosomes. Based on the specific SSR markers, chromosome substitutions occurred in thirty-six lines, and six lines segregated alleles from the two parents or were homozygous for the allele from Chinese Spring. These substitution lines were used to evaluate Type II (spread within the head) and Type V (deoxynivalenol accumulation within kernels) scab resistance. The objective was to use the substitution lines to evaluate the effect of individual chromosomes of Sumai 3 on Type 11 and Type V scab resistance in the greenhouse. Significant differences in Type II scab resistance and deoxynivalenol (DON) levels among different Chinese Spring (Sumai 3) substitution lines were detected. Positive chromosome substitution effects on Type II scab resistance were found on chromosomes 2B, 3B. 6B, and 7A from Sumai 3. Chromosomes 3B and 7A also reduced DON accumulation within the kernels, while chromosomes IB, 2D, and 4D from Sumai 3 increased DON concentration. Chromosome 7A from Sumai 3 had the largest effect on resistance to scab spread and DON accumulation. Additional research is in progress on the scab resistance conferred by chromosome 7A.     

The in vitro effects of benzodiazepines on the rat diaphragm. Structure-activity relationships

The effect of three different subgroups of benzodiazepines on the indirectly evoked twitch tension was investigated in the in vitro rat phrenic nerve - hemidiaphragm preparation. Two effects were observed: an initial increase in twitch tension at lower concentrations with some benzodiazepines, and a concentration-dependent depression at higher concentrations with all benzodiazepines. Significant differences for these effects were observed among the three subgroups of benzodiazepines and additionally within the subgroup of the 1,4-benzodiazepine-2-ketones. Structural requirements for both effects were different. For the increase of twitch tension a --CH3 substitution at R1 and a --F substitution at R2' were beneficial. For the twitch depression an --OH substitution at R3 and a --C1 substitution at R2' were optimal. An interaction between substituents at different substitution sites occurred. The potency of twitch depression showed a good correlation with literature reports of pKa values and a poor-to-inverse correlation with lipophilicity indices. A benzodiazepines antagonist, Ro 15-1788, caused no change in twitch tension in the concentration range of the investigated benzodiazepines nor did it prevent the twitch depression caused by benzodiazepines.     

Structural topological analysis of spike proteins of SARS-CoV-2 variants of concern highlight distinctive amino acid substitution patterns

Since the onset of pandemic in 2019, SARS-CoV-2 has diverged into numerous variants driven by antigenic and infectivity-oriented selection. Some variants have accumulated fitness-enhancing mutations, evaded immunity and spread despite global vaccination campaigns. The spike (S) glycoprotein of SARS-CoV-2 demonstrated the greatest immunogenicity and amino acid substitution diversity owing to its importance in the interaction with human angiotensin receptor 2 (hACE2). The S protein consistently emerges as an amino acid substitution (AAS) hotspot in all six lineages, however, in Omicron this enrichment is significantly higher. This study attempts to design and validate a method of mapping S-protein substitution profile across variants to identify the conserved and AAS regions. A substitution matrix was created based on publicly available databases, and the substitution localization was illustrated on a cryo-electron microscopy generated S-protein model. Our analyses indicated that the diversity of N-terminal (NTD) and receptor-binding (RBD) domains exceeded that of any other regions but still contained extended low substitution density regions particularly considering significantly broader substitution profiles of Omicron BA.2 and BA.4/5. Finally, the substitution matrix was compared to a random sample alignment of variant sequences, revealing discrepancies. Therefore, it was suggested to improve matrix accuracy by processing a large number of S-protein sequences using an automated algorithm. Several critical immunogenic and receptor-interacting residues were identified in the conserved regions within NTD and RBD. In conclusion, the structural and topological analysis of S proteins of SARS-CoV-2 variants highlight distinctive amino acid substitution patterns which may be foundational in predicting future variants.     

Molecular evolution of nuclear genes in Cupressacea, a group of conifer trees

We surveyed the molecular evolutionary characteristics of 11 nuclear genes from 10 conifer trees belonging to the Taxodioideae, the Cupressoideae, and the Sequoioideae. Comparisons of substitution rates among the lineages indicated that the synonymous substitution rates of the Cupressoideae lineage were higher than those of the Taxodioideae. This result parallels the pattern previously found in plastid genes. Likelihood-ratio tests showed that the nonsynonymous-synonymous rate ratio did not change significantly among lineages. In addition, after adjustments for lineage effects, the dispersion indices of synonymous and nonsynonymous substitutions were considerably reduced, and the latter was close to 1. These results indicated that the acceleration of evolutionary rates in the Cupressoideae lineage occurred in both the nuclear and plastid genomes, and that generally, this lineage effect affected synonymous and nonsynonymous substitutions similarly. We also investigated the relationship of synonymous substitution rates with the nonsynonymous substitution rate, base composition, and codon bias in each lineage. Synonymous substitution rates were positively correlated with nonsynonymous substitution rates and GC content at third codon positions, but synonymous substitution rates were not correlated with codon bias. Finally, we tested the possibility of positive selection at the protein level, using maximum likelihood models, assuming heterogeneous nonsynonymous-synonymous rate ratios among codon (amino acid) sites. Although we did not detect strong evidence of positively selected codon sites, the analysis suggested that significant variation in nonsynonymous-synonymous rate ratio exists among the sites. The most likely sites for action of positive selection were found in the ferredoxin gene, which is an important component of the apparatus for photosynthesis.     

“缺体回交法”选育普通小麦异代换系方法的研究

利用从蓝单体自交分离得到的自花结实的4D缺体小麦(缺72180、缺天选15)作母本与3个不同的八倍体小偃麦(小偃784、小偃7631和小偃78829)杂交,再以缺体作为轮回亲本,从F_1或F_2开始连续回交1—2次,在回交中,缺体无论作父本或母本都得到了异代换系,并且发现:(1)在回交过程中,用缺体作母本比作父本更为有效;(2)F_1自交,在F_2群体中选择生长比较正常,染色体数比较少的植株回交,比F_1作母本直接回交效果更好。并对所得的异代换系的特征特性进行了初步的观察研究,发现中间偃麦草(Agropyron intermedium2n=42) 4E染色体(以下用4Ei表示)、长穗偃麦草(Agropyron clongatum 2n=70)的4E染色体(带蓝粒基因,以下用4Ee表示)和4F染色体(带毛叶基因,以下用4Fe表示)均能正常补偿小麦4D染色体。异代换系生长旺盛,育性正常。初步总结了缺体与八倍体小偃麦杂交,回交过程中异代换系的形成规律,证明了“缺体回交法”可以推广应用于八倍体小偃麦等人工合成的新物种,以选育普通小麦异代换系。     

Nucleotide Sequence Analysis of Recent Epidemic Strains of Enterovirus 70

Nucleotide sequences of the genome of enterovirus 70 (EV70) isolated in Osaka in 1993 were determined, and compared with those of the past epidemic strains. Nucleotide substitution rates in 332 bp, 174 bp, and 178 bp of the genes encoding viral protein (VP)1, VP2, or VP3 were 9.0, 7.5, and 5.6% between Kumoi-2/93 and J670/71, respectively. Likewise, the putative amino acid substitution rates were 1.8, 0, and 0%. It seems that the epidemic strains of EV70 in Japan have been evolving at a constant high nucleotide substitution rate but almost all the substitutions were synonymous.     

On the estimation of the rate of nucleotide substitution for the control region of human mitochondrial DNA

To apply molecular clock for studying human evolution, the pattern of nucleotide substitution for the control region of human mtDNA was analyzed in detail. It is well known that the rate of nucleotide substitution for the control region is much higher than that for any other part of mtDNA. In this study, the higher substitution rate was attributed to the higher rate of transition-type substitution between pyrimidines within the D-loop part, whereas the rates of other types of substitution were essentially the same over the entire mtDNA molecule. Even within the control region, the rate and pattern of nucleotide substitution were different between the D-loop part and the rest. The rate and pattern for the non-D-loop part were very similar to those for fourfold-degenerate sites in the protein-coding region. In contrast, the D-loop and non-D-loop parts showed similarities in the base composition, whereas the base composition of fourfold-degenerate sites slightly different from that of the both parts of the control region. It is concluded, therefore, that the nucleotide frequencies of the control region should be used to estimate the number of substitutions (d) between the control region sequences. However, a method to verify the accuracy of the estimation of d by means of the transition/transversion (s/v) ratio was theoretically studied. It was suggested that the s/v ratio becomes constant over a wide range of d values only when the estimation of d is unbiased. On the basis of this result, the estimates of d previously obtained between human sequences were evaluated.     

Prevalence of Ile-460-Val/ParE Substitution in Clinical Streptococcus pneumoniae Isolates That Were Less Susceptible to Fluoroquinolones

A total of 73 clinical isolates of Streptococcus pneumoniae were measured for susceptibilities to nine fluoroquinolones, and nucleotide sequences of the quinolone resistance-determining regions (QRDRs) were determined. MIC₉₀s of sparfloxacin, tosufloxacin, grepafloxacin, and gatifloxacin were less than 0.5 mg/L and the MIC₉₀ of ciprofloxacin was 2 mg/L, although MIC values of some isolates to ciprofloxacin were more than 2 mg/L. We found that 60 of 73 isolates had only Ile-460-Val/ParE substitution and two isolates had an additional substitution of Ser-114-Gly/GyrA, while none of the isolates had any other substitutions in QRDRs of either ParC/E or GyrA/B. The isolates carrying Ile-460-Val/ParE substitution were more resistant to the fluoroquinolones norfloxacin and ciprofloxacin than the isolates with no amino acid substitution and the differences in MIC values were significant, suggesting that Ile-460-Val/ParE substitution in recent clinical S. pneumoniae isolates should be involved in the low-level fluoroquinolone resistance.