Recognition sequences of restriction endonucleases and methylases--a review

The properties and sources of all known endonucleases and methylases acting site-specifically on DNA are listed. The enzymes are crossindexed (Table I), classified according to homologies within their recognition sequences (Table II), and characterized within Table II by the cleavage and methylation positions, the number of recognition sites on the DNA of the bacteriophages lambda, phi X174 and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328 and the microorganisms from which they originate. Other tabulated properties of the restriction endonucleases include relaxed specificities (Table III), the structure of the restriction fragment ends (Table IV), and the sensitivity to different kinds of DNA methylation (Table V). Table VI classifies the methylases according to the nature of the methylated base(s) within their recognition sequences. This table also comprises those restriction endonucleases, which are known to be inhibited by the modified nucleotides. Furthermore, this review includes a restriction map of bacteriophage lambda DNA based on sequence data. Table VII lists the exact nucleotide positions of the cleavage sites, the length of the generated fragments ordered according to size, and the effects of the Escherichia coli dam- and dcmI-coded methylases M X Eco dam and M X Eco dcmI on the particular recognition sites.     

Table of Contents of Volume 51 - 2003

Table of Contents

Table of Contents of Volume 51 - 2003     

Table of Contents of Volume 52 - 2004

Table of Contents

Table of Contents of Volume 52 - 2004     

根癌农杆菌介导小麦幼胚遗传转化的影响因素

利用携带pC3301质粒(含bar和gus基因)的超毒根癌农杆菌菌株EHA105对普通小麦(Triticum aestivum L.)扬麦158进行了遗传转化,对筛选中的抗生素浓度、菌液浓度、共培养温度和时间、幼胚预培养时间、乙酰丁香酮(AS)浓度、洗涤用液及筛选方式等影响转化的几个重要因素进行了讨论.对从294个小麦幼胚外植体中转化得到的5株成活植株进行了PCR和Southern blot分析,结果表明其中2株小麦基因组中整合了外源DNA,转化频率为0.68%.     

Specificity of restriction endonucleases and DNA modification methyltransferases a review (Edition 3)

The properties and sources of all known class-I, class-II and class-III restriction endonucleases (ENases) and DNA modification methyltransferases (MTases) are listed and newly subclassified according to their sequence specificity. In addition, the enzymes are distinguished in a novel manner according to sequence specificity, cleavage position and methylation sensitivity. Furthermore, new nomenclature rules are proposed for unambiguously defined enzyme names. In the various Tables, the enzymes are cross-indexed alphabetically according to their names (Table I), classified according to their recognition sequence homologies (Table II), and characterized within Table II by the cleavage and methylation positions, the number of recognition sites on the DNA of the bacteriophages lambda, phi X174, and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328, and the microorganisms from which they originate. Other tabulated properties of the ENases include relaxed specificities (integrated within Table II), the structure of the generated fragment ends (Table III), interconversion of restriction sites (Table IV) and the sensitivity to different kinds of DNA methylation (Table V). Table VI shows the influence of class-II MTases on the activity of class-II ENases with at least partially overlapping recognition sequences. Table VII lists all class-II restriction endonucleases and MTases which are commercially available. The information given in Table V focuses on the influence of methylation of the recognition sequences on the activity of ENases. This information might be useful for the design of cloning experiments especially in Escherichia coli containing M.EcodamI and M.EcodcmI [H16, M21, U3] or for studying the level and distribution of site-specific methylation in cellular DNA, e.g., 5'- (M)CpG-3' in mammals, 5'-(M)CpNpG-3' in plants or 5'-GpA(M)pTpC-3' in enterobacteria [B29, E4, M30, V4, V13, W24]. In Table IV a cross index for the interconversion of two- and four-nt 5'-protruding ends into new recognition sequences is complied. This was obtained by the fill-in reaction with the Klenow (large) fragment of the E. coli DNA polymerase I (PolIk), or additional nuclease S1 treatment followed by ligation of the modified fragment termini [P3]. Interconversion of restriction sites generates novel cloning sites without the need of linkers. This should improve the flexibility of genetic engineering experiments [K56, P3].(ABSTRACT TRUNCATED AT 400 WORDS)     

Correction to: Quantification of the contrasting root systems of Pinus thunbergii in soils with different groundwater levels in a coastal forest in Japan

Plant and Soil - The original version of this article unfortunately contained a mistake. Table 3 was published erroneously. This Table has now been corrected.     

不同植物在水分胁迫条件下脯氨酸的累积与抗旱性的关系

Ca植物春小麦幼苗叶片累积脯氨酸的数量随水分胁迫时间和强度递增,累积的数量与品种的抗旱性没有相关性。C_4植物玉米和高粱累积脯氨酸的数量低于小麦,但高粱多于玉米。CAM植物落地生根脯氨酸含量略有变化。旱生植物细枝岩黄芪的同化枝累积脯氨酸的数量高于中生植物钻天杨和槐的叶片,而梭梭的同化校则低于槐而高于钻天杨。表明这些植物累积脯氨酸的数量与它们的抗旱性无夫。因此似不宜用脯氨酸数量的多少作为植物抗旱性的生理指标。     

Specificity of restriction endonucleases and methylases--a review

The properties and sources of all known restriction endonucleases and methylases are listed. The enzymes are cross-indexed (Table I), classified according to their recognition sequence homologies (Table II), and characterized within Table II by the cleavage and methylation positions, the number of recognition sites on the double-stranded DNA of the bacteriophages lambda, phi X174 and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328, and the microorganisms from which they originate. Other tabulated properties of the restriction endonucleases include relaxed specificities (integrated into Table II), the structure of the generated fragment ends (Table III), and the sensitivity to different kinds of DNA methylation (Table V). In Table IV the conversion of two- and four-base 5'-protruding ends into new recognition sequences is compiled which is obtained by the fill-in reaction with Klenow fragment of the Escherichia coli DNA polymerase I or additional nuclease S1 treatment followed by ligation of the modified fragment termini [P3]. Interconversion of restriction sites generates novel cloning sites without the need of linkers. This should improve the flexibility of genetic engineering experiments. Table VI classifies the restriction methylases according to the nature of the methylated base(s) within their recognition sequences. This table also comprises restriction endonucleases which are known to be inhibited or activated by the modified nucleotides. The detailed sequences of those overlapping restriction sites are also included which become resistant to cleavage after the sequential action of corresponding restriction methylases and endonucleases [N11, M21]. By this approach large DNA fragments can be generated which is helpful in the construction of genomic libraries. The data given in both Tables IV and VI allow the design of novel sequence specificities. These procedures complement the creation of universal cleavage specificities applying class IIS enzymes and bivalent DNA adapter molecules [P17, S82].     

T-DNA插入产生的水稻迟抽穗突变体的遗传分析

在筛选和鉴定水稻T-DNA插入纯合体的过程中,观察到一个迟抽穗的突变体.对该突变体进行遗传分析的结果表明,分离群体后代中出现正常抽穗、迟抽穗和特迟抽穗3种类型,分离比率为1:2:1,符合一对基因的不完全显性遗传;对突变体及其后代分离群体做Basta抗性检测及PCR分子检测,证实该突变体是由T-DNA插入所引起的,突变性状与T-DNA共分离.该材料可用于插入座位的基因克隆.     

Correction to: Smoke-saturated Water and Karrikinolide Modulate Germination,Growth, Photosynthesis and Nutritional Values of Carrot (Daucus carota L.)

Journal of Plant Growth Regulation - The original version of this article unfortunately contained a mistake in Table 3. The correct Table is given below.     

Evaluating the dendroclimatological potential of central Appalachian Table Mountain pine (Pinus pungens LAMB.)

Table Mountain pine (Pinus pungens Lamb.) is an Appalachian endemic that occurs in a patchy distribution from Georgia to Pennsylvania on xeric, fire-prone sites. Beginning in the 1990s, Table Mountain pine first showed usefulness in reconstructing fire regimes in these xeric Appalachian forests. The next step in Table Mountain pine research, the relationships between fire occurrence and climate variables, cannot happen until the dendrochronological potential of the species has been proven. This research investigates the annual ring structure and formation, relationship between climate and growth, and dendrochronological dating between trees in the same stands to prove the species’ effectiveness in climate reconstructions. Table Mountain pine cores and cross-sections were collected from four sites in the Virginia Appalachian Mountains. Results indicate that the species is sensitive to climate (monthly precipitation and temperature, PDSI and PHDI). Climate analyses revealed that Table Mountain pine growth is reduced when the previous year's September is drier than normal, the current year’s February is wetter than average, and the winter is colder than average. Results of these climate analyses illustrate a regional climate signal in Table Mountain pine stands; however, results from individual sites provided more significant details on the influence of climate on the species.     

Early cellular alterations induced by myocardial hypoxia: possible role of cyclic AMP (author's transl)

The ability of endogenous myocardial catecholamines to participate in the development of myocardial cellular alterations during a short period of severe hypoxia (30 min) was studied in isolated, Langendorff-perfused rat heart preparation, arrested by a high potassium concentration (16 mM) and perfused in the absence of exogenous substrate (Table I). Tyramine, which accelerated catecholamine depletion, also increased myocardial cell damage as assessed by a higher lactate dehydrogenase (LDH) release and a more marked reduction in cellular levels of high energy phosphates and glycogen (Table II). On the other hand, under conditions of beta-blockade (atenolol), hypoxia-induced tissular damage was reduced (Table II). These changes could be related to modifications in the cellular content of cyclic AMP (cAMP) since cAMP was consistently higher during the first 30 min of hypoxic perfusion than in control normoxic hearts (Table III) whereas cyclic GMP content remained unchanged. Moreover, interventions increasing cellular content of cAMP (theophylline, dibutyryl-cAMP) also increased hypoxic damage (Table IV), whereas N-methyl imidazole which reduced cellular content of cAMP lessened hypoxia-induced cellular alterations (Table IV). It is concluded that cellular lesions developing during the first 30 min of hypoxia in isolated arrested rat heart preparation perfused without exogenous substrate could be related to intracellular accumulation of cAMP occurring under the effect of endogenous catecholamine release.     

Quantification of endocytosis-derived membrane traffic

The main data covered by this article have been summarized in Table I. A fairly uniform picture is obtained for endocytosis-derived membrane transfer and compartmentation. This may be due to the limited amount of information and the resulting low resolution. Data on mainly three cell types are presented: macrophages, fibroblasts and amoebae. The data vary as much for one cell type as between different cells. Therefore, no possible differences related to cell function emerge. More detailed data, for more cell types, may change the picture. The values for cell surface area, although significantly different in absolute terms (column S in Table I), are rather similar when related to cell diameter, all being about 3-fold in excess of the surface area of the smooth sphere of comparable volume (column xi in Table I). The rate of plasma membrane internalization for macrophages and amoebae both professional phagocytes, is about 2 cell surface area equivalents per h or more. This may be somewhat higher than for fibroblasts (column PM/h in Table I). The average residence time for membrane on the cell surface, therefore, is about 30 min. A most interesting finding seems to be the rather uniform values obtained for the average size (volume weighted) of primary pinosomes, being about 0.3 micron in diameter (column phi-Internalization in Table I). Due to their rapid increase in size as a result of fusion (cf. Fig. 2), it has not been feasible to directly measure the size of primary pinosomes by morphometric means. The values in Table I, give no information on the size distributions of primary pinosomes and on whether these consist of one or more size classes. The steady-state average diameter of pinosomes is noticeably larger than that of primary pinosomes (column phi-pinosomes in Table I; cf. Table II for Acanthamoebae). The corresponding decrease in surface-to-volume ratio can make about 50% of pinosomal membrane available for recycling directly from this membrane compartment. Membrane recycling from the pinosomal compartment occurs after an average residence time of about 3 min for macrophages and 4-6 min for fibroblasts (column tau-pinosomes in Table I). The relative pool size of intracellular membranes participating in shuttling to and from the cell surface is significantly different for animal cells and amoebae (column rho in Table I). For macrophages, fibroblasts, CHO cells, and mast cells, this intracellular membrane pool amounts to about 10-20% the plasma membrane area, compared to 150-200% in the case of amoebae.(ABSTRACT TRUNCATED AT 400 WORDS)     

Correction to: Periodic inundations drive community assembly of amphibious plants in floodplain lakes

Hydrobiologia - Due to an unfortunate mistake during the production process, some rows in Table 1 were distorted. The original article has been corrected and the correct display of Table 1 is also...     

Mechanisms of Retrovirus pathogenicity

The number of identified human retroviruses (HRV) is increasing (Table 1) as is the number of disease associated with them (Table 2). Here we present a synthetic overview of the mechanisms of disease production by known HRV as presently understood.     

ERRATA

P. 65, line 8, for 86-215 lx read 8,50-21,50 lx P. 66, Table I, for 96 lx read 9,600 lx Table 2, All valuesof light intensity to be multiplied by 100 line 16, for 107lx read 10,700 lx line 17, for 107 lx read 10,700 lx P. 67, Table 3, All values of light intensity to be multipliedby 100 P. 68, Table 4, All values of light intensity to be multipliedby 100 Table 5, All values of light intensity to be multipliedby 100     

EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species

Following the publication of our recent article (Kapp et al., BMC Genomics 2006, 7:231), we (the authors) regrettably found several errors in the published Table 5. This correction article not only describes what makes the published Table 5 incorrect, it also presents the correct Table 5.     

Inhibition of NF-κB activation by the histone deacetylase inhibitor 4-Me2N-BAVAH induces an early G1 cell cycle arrest in primary hepatocytes

The authors would like to draw the readers' attention to the fact that in the above article, an incorrect version of Table 1 was published. The correct version of Table 1 is printed below:     

怒江上游三种裂腹鱼类摄食及消化器官比较研究

于2017年5和6月以及9和10月在怒江西藏段收集了怒江裂腹鱼（Schizothorax nukiangensis）194尾、裸腹叶须鱼（Ptychobarbus kaznakovi）152尾,热裸裂尻鱼（Schizopygopsis thermalis）117尾。综合运用3 种多元分析方法分析3 种鱼类摄食及消化器官形态的种间差异,结果显示,主要种间差异部位为头部及肠道;种间形态指标均为显著性差异（P < 0.05）;3种裂腹鱼的头部形态已有了一定程度的分化。鱼类食物组成及食物竞争情况研究表明,怒江裂腹鱼和裸腹叶须鱼属杂食性偏动物食性鱼类,两者食物重叠指数较高（0.91）;热裸裂尻鱼属杂食性偏植物食性鱼类。食物多样性指数的种间差异明显。3种裂腹鱼营养及空间生态位均有分化,摄食与水温、流速和海拔等环境因素密切相关。     

Effect of liming on EUF-nutrient fractions in the soil,on nutrient contents of grape leaves and on grape yield

Summary In pot experiments with vine, liming significantly raised EUF-Ca 20°C as well as EUF-Ca 80°C values of an acid clay soil (pH 4.2). This resulted in a marked rise in Ca contents of vine leaves (Table 2). High amounts of K fertilizers without lime raised mainly the EUF-Ca 20°C values whereas the EUF-80°C values remained at a low level (Table 3). Liming lowered the EUF-K 20°C values and as a result the ratio EUF-K 80°C C/EUF-K 20°C increased from 0.7 to 1.0.High K applications raised the K content of the leaves at flowering stage but at grape ripening a marked decrease in K content was observed (Table 5). In contrast, the application of both lime and K fertilizer raised the K content of leaves at both flowering and ripening. Grape yield increased as well (Table 11).Liming raised the EUF-P values of the soil and to a lesser extent the P contents of leaves (Tables 6 and 7).High K applications without lime raised the Mn contents of leaves (Table 9), Exchange processes due to K fertilizer addition were reflected in increased EUF-Mn values (Table 9).The highest yield (three-year average) was obtained in a high K treatment (22 g K₂O/pot) in combination with lime (40 g CaO/pot).