Deciphering apicoplast targeting signals – feature extraction from nuclear-encoded precursors of Plasmodium falciparum apicoplast proteins

The malaria causing protozoan Plasmodium falciparum contains a vestigal, non-photosynthetic plastid, the apicoplast. Numerous proteins encoded by nuclear genes are targeted to the apicoplast courtesy of N-terminal extensions. With the impending sequence completion of an entire genome of the malaria parasite, it is important to have software tools in place for prediction of subcellular locations for all proteins. Apicoplast targeting signals are bipartite; containing a signal peptide and a transit peptide. Nuclear-encoded apicoplast protein precursors were analyzed for characteristic features by statistical methods, principal component analysis, self-organizing maps, and supervised neural networks. The transit peptide contains a net positive charge and is rich in asparagine, lysine, and isoleucine residues. A novel prediction system (PATS, predict apicoplast-targeted sequences) was developed based on various sequence features, yielding a Matthews correlation coefficient of 0.91 (97% correct predictions) in a 40-fold cross-validation study. This system predicted 22% apicoplast proteins of the 205 potential proteins on P. falciparum chromosome 2, and 21% of 243 chromosome 3 proteins. A combination of the PATS results with a signal peptide prediction yields 15% potentially nuclear-encoded apicoplast proteins on chromosomes 2 and 3. The prediction tool will advance P. falciparum genome analysis, and it might help to identify apicoplast proteins as drug targets for the development of novel anti-malaria agents.     

飞行状态下四种菊头蝠回声定位声波的小波包识别方法

研究了飞行状态下的四种菊头蝠回声定位声波的识别方法.通过小波包分解得到各个频带能量作为识一别特征向量,用主成分分析法优化特征空间.提取少数几个主成分,这些主成分彼此不相关,符合特征优化的要求,以主成分向量作为BP神经网络的输入对蝙蝠的种类进行识别.个体识别正确率达到了80%以上,表明基于小渡包分解和神经网络识别的方法对蝙蝠回声定位声波进行识别是可行的.     

恶性疟原虫abstrakt同源基因的克隆及DEAD盒家族蛋白的序列分析

DEAD盒蛋白家族的ATP依赖性的RNA解旋酶类参与细胞内几乎所有的RNA代谢过程 ,在几乎所有生物的细胞生长发育过程中扮演着众多不可或缺的角色。在本实验中 ,通过PCR和探针杂交相结合的筛选方法 ,筛选恶性疟原虫 (Plasmodiumfalciparum)的基因组文库 ,克隆了FH1F———abstrakt同源基因的完整序列。通过搜索已经完成测序的恶性疟原虫基因组数据库 ,推测FH1F序列定位在第 5条染色体上。FH1F全长2 80 4bp,包含一个 1 1 6 1bp的完整阅读框 ,编码一个由 386个氨基酸组成的蛋白。对FH1F蛋白序列用BlastP进行搜索和分析以及用DNAStar与许多典型的DEAD盒蛋白序列进行比对分析 ,结果均提示FH1F蛋白应该是DEAD盒家族的一个Abstrakt蛋白。另一方面 ,用DNAStar对已知所有完整的DEAD盒蛋白进行详细的序列分析以及用Mega对这些序列进行系统发育研究的结果都显示 :DEAD盒家族的蛋白聚类成为若干不同的亚群 ;与DEAD盒蛋白的一般保守序列相比 ,Abstrakt,eIF 4A ,Vasa ,P6 8等不同亚群的DEAD盒蛋白在保守区具有各自不同的结构特征。本文对不同的DEAD盒蛋白的结构特征进行了总结并试图给出不同亚群分类上的结构标准 ,对Abstrakt蛋白在本应高度保守的位点上异常于其它DEAD盒蛋白的氨基酸残基的取代也进行了相关的初步分析     

北京地区中华姬鼠与大林姬鼠的数量分类研究

利用主成分分析、系统聚类分析和非参数检验,对采自北京地区的88只姬鼠标本（黑线姬鼠Apodemus agrarius除外）的10个形态分类指标进行了分析,以便确定出最具种问特异性的形态分类特征并给出定量判别标准．结果表明：除黑线姬鼠外,北京地区另有中华姬鼠（A．draco）和大林姬鼠（A．peninsulae）两种姬鼠;门齿孔后缘距上臼齿列前缘水平线的距离（x9）、上领M^1后内侧齿突向舌侧突出的程度（x1）及其与第2横嵴内侧齿突的相对大小（x2）是区分后两种姬鼠的最有效的形态分类指标;3个指标的种间界限大致为：中华姬鼠x9〈0．4mm,01≥0．2mm,x2≥0．6;大林姬鼠x9≥0．4mm,x1〈0．2mm,x2〈0．6．     

Seasonal and Geographical Influences on the Chemical Composition of Juniperus phoenicea L. Essential Oil Leaves from the Northern Tunisia

The essential‐oil composition of 60 individual trees of Juniperus phoenicea L. from four Tunisian populations in three different periods were investigated by GC and GC/MS analyses. 59 Compounds were identified in the oils, and a relatively high variation in their contents was found. All the oils were dominated by the terpenic hydrocarbon fraction, and the main component was α‐pinene (20.28–40.86%). The results of the oil compositions were processed by hierarchical clustering and principal component analysis (PCA) allowing establishing four groups of essential‐oils differentiated by one compound or more. Pattern of geographic variation in essential‐oil composition indicated that individuals from the continental site (Makthar) were clearly distinguished from those from littoral localities (Tabarka, Hawaria, and Rimel).     

Chemical variations of the essential oils in flower heads of Chrysanthemum indicum L. from China

The volatile compositions of hydrodistilled essential oils in the flower heads of Chrysanthemum indicum L. from eight populations in China were analyzed by GC/MS. A total of 169 compounds representing 88.79-99.53% of the oils were identified, and some remarkable differences were found in the constituent percentages of the eight populations. The predominant components of the essential oils were 1,8-cineole (0.62-7.34%), (+)-(1R,4R)-camphor (0.17-27.56%), caryophyllene oxide (0.54-5.8%), β-phellandrene (0.72-1.87%), (-)-(1S,2R,4S)-borneol acetate (0.33-8.46%), 2-methyl-6-(p-tolyl)hept-2-ene (0.3-8.6%), 4,6,6-trimethylbicyclo[3.1.1]hept-3-en-2-yl acetate (0.17-26.48%), and hexadecanoic acid (0.72-15.97%). The chemotaxonomic value of the essential-oil compositions was discussed according to the results of cluster analysis (CA) and principal-component analysis (PCA). The eight populations were divided into five groups as different chemotypes (Groups A-E), and the scores together with the loadings revealed clearly different chemical properties of each population. In conclusion, GC/MS in combination with chemometric techniques provided a flexible and reliable method for characterizing the essential oils of different populations of C. indicum L.     

Variability of the Needle Essential Oils of Juniperus deltoides R.P.Adams from Different Populations in Serbia and Croatia

The essential‐oil compositions of one Croatian and three Serbian populations of Juniperus deltoides R.P.Adams have been determined by GC/MS analysis. In total, 147 compounds were identified, representing 97.3–98.3% of the oil composition. The oils were dominated by monoterpenes, which are characteristic components for the species of the section Juniperus. Two monoterpenes, α‐pinene and limonene, were the dominant constituents, with a summed‐up average content of 49.45%. Statistical methods were used to determine the diversity of the terpene classes and the common terpenes between the newly described J. deltoides populations from Serbia and Croatia. Only reports on several specimens from this species have been reported so far, and there are no studies that treat population diversity. Cluster analysis of the oil contents of 21 terpenes showed high correlation with the geographical distribution of the populations, separating the Croatian from the Serbian populations. The comparison of the essential‐oil compositions obtained in the present study with literature data, showed the separation of J. deltoides and J. oxycedrus ssp. oxycedrus from the western Mediterranean region.     

Chemical Variability of Xylopia quintasii Engl. & Diels Leaf Oil from Côte d'Ivoire

The chemical composition of 42 essential‐oil samples isolated from the leaves of Xylopia quintasii harvested in three Ivoirian forests was investigated by GC‐FID, including the determination of retention indices (RIs), and by ¹³C‐NMR analyses. In total, 36 components accounting for 91.9–92.6% of the oil composition were identified. The content of the main components varied drastically from sample to sample: (E)‐β‐caryophyllene (0.9–56.9%), (Z)‐β‐ocimene (0.3–54.6%), β‐pinene (0.8–27.9%), α‐pinene (0.1–22.8%), and furanoguaia‐1,4‐diene (0.0–17.6%). The 42 oil compositions were submitted to hierarchical cluster and principal components analysis, which allowed the distinction of three groups within the oil samples. The composition of the oils of the major group (22 samples) was dominated by (E)‐β‐caryophyllene. The oils of the second group (12 samples) contained β‐pinene and α‐pinene as the principal compounds, while the oils of the third group (8 samples) were dominated by (Z)‐β‐ocimene, germacrene D, (E)‐β‐ocimene, and furanoguaia‐1,4‐diene. The oil samples of Group I and II came from clay‐soil forests, while the oil samples belonging to Group III were isolated from leaves harvested in a sandy‐soil forest.     

Chemical Variability of the Leaf Essential Oil of Xylopia aethiopica (Dunal) A.Rich. from Côte d'Ivoire

The chemical composition of 48 essential‐oil samples isolated from the leaves of Xylopia aethiopica harvested in six Ivoirian forests was investigated by GC‐FID and ¹³C‐NMR analyses. In total, 23 components accounting for 82.5–96.1% of the oil composition were identified. The composition was dominated by the monoterpene hydrocarbons β‐pinene (up to 61.1%) and α‐pinene (up to 18.6%) and the sesquiterpene hydrocarbon germacrene D (up to 28.7%). Hierarchical cluster and principal component analyses allowed the distinction of two groups on the basis of the β‐pinene and germacrene D contents. The chemical composition of the oils of Group I (38 oil samples) was clearly dominated by β‐pinene, while those of Group II (10 samples) were characterized by the association of β‐pinene and germacrene D. The leaves collected in the four inland forests produced β‐pinene‐rich oils (Group I), while the oil samples belonging to Group II were isolated from leaves harvested in forests located near the littoral.     

Variability in the Essential‐Oil Composition of Sideritis scardica Griseb. from Native Bulgarian Populations

The essential‐oil composition of six native populations of Sideritis scardica from Bulgaria was studied by GC‐FID and GC/MS analyses. Altogether, 37 components, representing 73.1 to 79.2% of the total oil content were identified. Among them, α‐pinene (4.4–25.1%), β‐pinene (2.8–18.0%), oct‐1‐en‐3‐ol (2.3–8.0%), phenylacetaldehyde (0.5–9.5%), β‐bisabolene (1.3–11.0%), benzyl benzoate (1.1–14.3%), and m‐camphorene ( 1 ; 0.3–12.4%) were the main compounds. All samples were characterized by low contents of oxygenated mono‐ and sesquiterpenes (≤1.6 and 2.3%, resp.). Principal component analysis (PCA) and cluster analysis (CA) showed a significant variability in the chemical composition of the studied samples as well as a correlation between the oil profiles and the ecological conditions of the natural habitats of S. scardica.     

Chemical Variability of Cleistopholis patens (Benth.) Engl. et Diels Leaf Oil from Ivory Coast

The chemical composition of 48 leaf oil samples isolated from individual plants of Cleistopholis patens (Benth .) Engl. et Diels harvested in four Ivoirian forests was investigated by GC‐FID (determination of retention indices), GC/MS, and ¹³C‐NMR analyses. The main components identified were β‐pinene (traces–59.1%), sabinene (traces–54.2%), (E)‐β‐caryophyllene (0.3–39.3%), linalool (0.1–38.5%), (E)‐β‐ocimene (0.1–33.2%), germacrene D (0.0–33.1%), α‐pinene (0.1–32.3%), and germacrene B (0–21.2%). The 48 oil compositions were submitted to hierarchical clustering and principal components analyses, which allowed the distinction of three groups within the oil samples. The oil composition of the major group (Group I, 33 samples) was dominated by (E)‐β‐caryophyllene and linalool. The oils of Group II (eight samples) contained mainly β‐pinene and α‐pinene, while those of Group III (seven samples) were dominated by sabinene, limonene, and β‐phellandrene. Moreover, the compositions of the Ivoirian C. patens leaf oils differed from those of Nigerian and Cameroonian origins.     

Essential‐Oil Composition and Chemical Variability of Senecio vulgaris L. from Corsica

The chemical composition of the essential oils isolated from the aerial parts of Senecio vulgaris plants collected in 30 Corsican localities was characterized using GC‐FID and GC/MS analyses. Altogether, 54 components, which accounted for 95.2% of the total oil composition, were identified in the 30 essential‐oil samples. The main compounds were α‐humulene ( 1 ; 57.3%), (E)‐β‐caryophyllene ( 2 ; 5.6%), terpinolene ( 3 ; 5.3%), ar‐curcumene ( 4 ; 4.3%), and geranyl linalool ( 5 ; 3.4%). The chemical composition of the essential oils obtained from separate organs and during the complete vegetative cycle of the plants were also studied, to gain more knowledge about the plant ecology. The production of monoterpene hydrocarbons, especially terpinolene, seems to be implicated in the plant‐flowering process and, indirectly, in the dispersal of this weed species. Comparison of the present results with the literature highlighted the originality of the Corsican S. vulgaris essential oils and indicated that α‐humulene might be used as taxonomical marker for the future classification of the Senecio genus. A study of the chemical variability of the 30 S. vulgaris essential oils using statistical analysis allowed the discrimination of two main clusters according to the soil nature of the sample locations. These results confirmed that there is a relation between the soil nature, the chemical composition of the essential oils, and morphological plant characteristics. Moreover, they are of interest for commercial producers of essential oil in selecting the most appropriate plants.     

Essential‐Oil Composition of the Fruits of Six Heracleum L. Species from Iran: Chemotaxonomic Significance

The fruit essential oils of Heracleum persicum, H. rechingeri, H. gorganicum, H. rawianum, H. pastinacifolium, and H. anisactis from Iran were obtained by hydrodistillation and characterized by GC‐FID and GC/MS analyses. The oils of the six species were compared to determine the similarities and differences among their compositions. Overall, 36 compounds were identified in the fruit oils, accounting for 92.40–96.74% of the total oil compositions. Aliphatic esters constituted the main fraction of the oils (86.61–94.31%), with octyl acetate and hexyl butyrate as the major components. The oil compositions of species belonging to section Pubescentia (H. persicum, H. gorganicum, and H. rechingeri) were discriminated by equally high contents of both octyl acetate (13.84–20.48%) and hexyl butyrate (17.73–38.36%). On the other hand, the oils of H. rawianum, H. pastinacifolium and H. anisactis, belonging to section Wendia, showed lower hexyl butyrate contents (3.62–6.6%) and higher octyl acetate contents (48.71–75.36%) than the former. Moreover, isoelemicin was identified at low amounts (0.10–2.51%) only in the oils of the latter species. The differences in the oil composition among the six species were investigated by hierarchical cluster and principal component analyses, which indicated that the oil composition confirmed well the taxonomical classification based on the morphological and botanical data, and, thus, may provide a reliable marker to discriminate Heracleum species at the intersectional level.     

Chemical Variability of the Essential Oil of Juniperus phoenicea var. turbinata from Algeria

The chemical composition of 50 samples of leaf oil isolated from Algerian Juniperus phoenicea var. turbinata L. harvested in eight locations (littoral zone and highlands) was investigated by GC‐FID (in combination with retention indices), GC/MS, and ¹³C‐NMR analyses. The composition of the J. phoenicea var. turbinata leaf oils was dominated by monoterpenes. Hierarchical cluster and principal component analyses confirmed the chemical variability of the leaf oil of this species. Indeed, three clusters were distinguished on the basis of the α‐pinene, α‐terpinyl acetate, β‐phellandrene, and germacrene D contents. In most oil samples, α‐pinene (30.2–76.7%) was the major compound, associated with β‐phellandrene (up to 22.5%) and α‐terpinyl acetate (up to 13.4%). However, five out of the 50 samples exhibited an atypical composition characterized by the predominance of germacrene D (16.7–22.7%), α‐pinene (15.8–20.4%), and α‐terpinyl acetate (6.1–22.6%).     

Volatiles of Curcuma mangga Val. & Zijp (Zingiberaceae) from Malaysia

Analysis by GC and GC/MS of the essential oil obtained from Malaysian Curcuma mangga Val. & Zijp (Zingiberaceae) rhizomes allowed the identification of 97 constituents, comprising 89.5% of the total oil composition. The major compounds were identified as myrcene (1; 46.5%) and β-pinene (2; 14.6%). The chemical composition of this and additional 13 oils obtained from selected Curcuma L. taxa were compared using multivariate statistical analyses (agglomerative hierarchical cluster analysis and principal component analysis). The results of the statistical analyses of this particular data set pointed out that 1 could be potentially used as a valuable infrageneric chemotaxonomical marker for C. mangga. Moreover, it seems that C. mangga, C. xanthorrhiza Roxb., and C. longa L. are, with respect to the volatile secondary metabolites, closely related. In addition, comparison of the essential oil profiles revealed a potential influence of the environmental (geographical) factors, alongside with the genetic ones, on the production of volatile secondary metabolites in Curcuma taxa.     

Chemical Variability of the Needle Oil of Juniperus communis ssp. alpina from Corsica

The composition of 109 samples of essential oil isolated from the needles of Juniperus communis ssp. alpina growing wild in Corsica was investigated by GC (in combination with retention indices), GC/MS, and ¹³C‐NMR. Forty‐four compounds accounting for 86.7–96.7% of the oil were identified. The oils consisted mainly of monoterpene hydrocarbons, in particular, limonene (9.2–53.9%), β‐phellandrene (3.7–25.2%), α‐pinene (1.4–33.7%), and sabinene (0.1–33.6%). The 109 oil compositions were submitted to k‐means partitioning and principal component analysis, which allowed the distinction of two groups within the oil samples. The composition of the major group (92% of the samples) was dominated by limonene and β‐phellandrene, while the second group contained mainly sabinene beside limonene and β‐phellandrene.     

Variability of the Root Essential Oils of Seseli rigidum Waldst. & Kit. (Apiaceae) from Different Populations in Serbia

The chemical compositions of the essential oils of seven natural populations of Seseli rigidum were analyzed. The essential‐oil yield ranged from 0.16 to 2.09%. Analysis of variance (ANOVA) revealed that there were no statistically significant differences in the mean essential‐oil yields between the populations, and no significant influence of the climate or soil type on the oil yield was observed. In all 67 analyzed samples, the polyacetylene falcarinol was the main compound, followed by octanal, methyl linoleate, α‐muurolene, 3‐butylphthalide, falcarinone, muurola‐4,10(14)‐dien‐1β‐ol, β‐sesquiphellandrene, salvial‐4(14)‐en‐1‐one, δ‐amorphene, spathulenol, and isospathulenol. The principal component analysis (PCA), the canonical discriminant analysis (CDA), and the cluster analysis (CA) revealed differentiation between the populations based on the climate. Three groups of populations were formed; the first group was composed of samples growing in regions with a humid climate, with oils having high falcarinol and low sesquiterpene contents, and the second and third groups comprised samples exposed to semi‐arid climate, with oils characterized by a lower falcarinol and higher α‐muurolene, δ‐amorphene, β‐sesquiphellandrene, and salvial‐4(14)‐en‐1‐one contents. The semi‐arid populations were divided into two groups, which were distinguished based on the oil contents of sesquiterpenes, falcarinone, and 3‐butylphthalide. On the other hand, no clear separation between populations based on the different soil types could be observed.     

Chemical Composition and Interpopulation Variability of Essential Oils of Taxus baccata L. from Serbia

The composition of the essential oil of the twigs and needles of Taxus baccata L. from three natural populations in Serbia has been determined by GC/MS analysis. Of the 91 detected compounds, 87 were identified. The most abundant compound classes were aliphatic alcohols, terpenes, aliphatic hydrocarbons, and aliphatic aldehydes, which together comprised ca. 86.92% of the total oil composition. The dominant constituents were oct‐1‐en‐3‐ol (23.48%), (3Z)‐hex‐3‐en‐1‐ol (11.46%; aliphatic alcohols), and myrtenol (11.38%; oxygenated monoterpene). The PCA of 22 selected compounds revealed differentiations of populations based on geographic distribution. The CA showed that Populations I and II from the Dinaric Alps were similar, and that Population III from the Balkan mountain system was distinct. This was the first investigation of interpopulation variability of T. baccata populations based on essential oil composition. The results of this study were compared with those of previous studies concerning volatile compounds produced by Taxus species. The results indicate that the essential oil content of T. baccata populations from this study is unique, mostly resembling the population from southeast Serbia.     

Biochemical Characterization of Helichrysum italicum (Roth) G.Don subsp. italicum (Asteraceae) from Montenegro: Phytochemical Screening,Chemotaxonomy, and Antioxidant Properties

The chemical composition and antioxidant properties of the essential oil and EtOH extract of immortelle (Helichrysum italicum (Roth) G.Don subsp. italicum, Asteraceae) collected in Montenegro were evaluated. The essential oil was characterized by GC/MS analysis, and the content of total phenolics and flavonoids in the EtOH extract was determined using the Folin? Ciocalteu reagent. The free‐radical‐scavenging capacity (RSC) of both the essential oil and the EtOH extract was assessed with the 2,2‐diphenyl‐1‐pycrylhydrazyl (DPPH) method. Moreover, the inhibition of hydroxyl radical (^.OH) generation by the EtOH extract of immortelle was evaluated for the first time here. Neryl acetate (28.2%) and γ‐curcumene (18.8%) were the main compounds in the essential oil, followed by neryl propionate (9.1%) and ar‐curcumene (8.3%). The chemical composition of the oils of the examined and additional 16 selected Helichrysum italicum taxa described in literature were compared using principal component (PCA) and cluster (CA) analyses. The results of the statistical analyses implied the occurrence of at least four different main and three subchemotypes of essential oils. Considering the antioxidant properties, the EtOH extract of immortelle exhibited similar potential as propyl gallate and quercetin, while the essential oil exhibited relatively weak DPPH^.‐scavenging capacity.