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.     

DOES LIGHT QUALITY AFFECT THE SINKING RATES OF MARINE DIATOMS?1

Although the spectral quality of light in the ocean varies considerably with depth, the effect of light quality on different physiological processes in marine phytoplankton remains largely unknown. In cases where experiments are performed under full spectral irradiance, the meaning of these experiments in situ is thus unclear. In this study, we determined whether variations in spectral quality affected the sinking rates of marine diatoms. Semicontinuous batch cultures of Thalassiosira weissflogii (Gru.) Fryxell et Hasle and Ditylum brightwellii (t. West) Grunow in Van Huerk were grown under continuous red, white, or blue light. For T. weissflogii, sinking rates (SETCOL method) were twice as high (～0.2 m·d^?1)for cells grown under red light as for cells grown under white or blue light (～0.08 m·d^?1), but there were no significant differences in carbohydrate content (～105 fg·μm^?3) or silica content (～ 17 fg·μ^?3) to account for the difference in sinking rates. Thalassiosira weissflogii grown under blue light was significantly smaller (495 μm³) than cells grown under red light (661 μm³), which could contribute to its reduced sinking rate. However, cells grown under white light were similar in size to those grown under red light but had sinking rates not different from those of cells grown under blue light, indicating the involvement of factors other than size. There were no significant differences in sinking rate (～0.054 m·d^?1) or silica content (～20 fg·μm^?3) in D. brightwellii grown under red, white, or blue light, but cells grown under red light were significantly (20%) larger and contained significantly (20%) more carbohydrate per μm³ than cells grown under white or blue light. Spectral quality had no consistent effect on sinking rate, biochemical composition (carbohydrate or silica content), or cell volume in the two diatoms studied. The similarity in sinking rate of cells grown under white light compared to those grown under blue light supports the ecological validity of sinking rate studies done under white light.     

Serological Characterization of Trichosporon cutaneum and Related Species

Recent molecular biological, chemical, physiological and morphological studies indicate that Trichosporon cutaneum and related species should be reclassified. In this study, antigenic characteristics of the species were determined. The results of adsorption experiments revealed that there were at least three serological types: I, II and III. Specific factor sera I, II and III were prepared on the basis of adsorption experiments and isolates were serotyped by cell slide agglutination (CSA). Since the CSA test was difficult to read in some strains, the results of the CSA test were compared with the findings from an enzyme-linked immunosorbent assay (ELISA). For the ELISA, crude polysaccharide antigens prepared from the culture supernatant were used as the antigen. The types determined by ELISA correlated well with those determined by the CSA test. These data suggest that T. cutaneum and related species have at least three serological types, and that the typing can be done by either CSA or ELISA.     

露水草的光合特性及其生态学意义

用盆栽和遮阴试验研究了露水草（Ｃｙａｎｏｔｉｓ ａｒａｃｈｎｏｉｄｅａ Ｃｌａｒｋｅ） 的光合作用特征,比较了不同遮光水平对光合速率、光合器官特性及光合产量的影响。结果如下：１．露水草是一种耐阴偏阳的Ｃ３ 类草木植物,其光合作用的光饱和点约为６５０ μｍ ｏｌ·ｍ － ２·ｓ－ １,光补偿点约为１７ μｍ ｏｌ·ｍ － ２·ｓ－ １,且具有高达１３０×１０－ ６的ＣＯ２ 补偿点。２．露水草的最大净光合速率为１２．４５ μｍ ｏｌ·ｍ － ２·ｓ－ １。叶片净光合速率的日变化规律呈双峰曲线,主峰在１１～１２ 时,次峰在１５时左右。３．遮光２０％ ～５０％ 有利于露水草的生长。与对照相比,叶片中叶绿素ｂ 的含量增加了４７％ ～８３％ ,并且由于净光合速率（相对光合速率）的提高,使光合生产量增加了１２％ ～１８％ 。     

马桑菌株的生物学特性

对从湖北、四川、云南等地采集的尼泊尔马桑(Coriaria nepalensis Wall.)根瘤中分离的20株内生菌纯培养物所进行的研究表明,其形态均具有弗兰克氏菌属的特征。在粗细不一的分枝菌丝体上有泡囊和孢囊,有的还有串珠状结构的菌丝体。不同菌株在液体培养基上生长速度很不一致;菌丝体多呈絮状或颗粒状沉淀,个别还呈薄膜状沉淀;绝大多数菌株的菌丝体具有不同色调的色素;在S培养基中大多数都能产生可溶性色素。上述这些培养特征常因培养基成分和培养方式的不同而有差异。大多数菌株的胞壁组分属Ⅱ型,少数菌株为Ⅲ型;全细胞糖型变化很大,20个菌株可划分为6个糖型,而且绝大多数糖型与已知弗兰克氏菌有所不同。此外,有65％的菌株还具有明显的抗菌活性。     

Alternating bolus and continuous infusion 5-fluorouracil: a strategy to overcome resistance to this fluoropyrimidine in advanced colorectal cancer patients

Focusing our effort on the importance of FUra scheduling we have tested the hypothesis that pulse and continuous infusion (CI) of the fluoropyrimidine have different mechanisms of cytotoxicity. Our initial approach was to compare the mechanism of resistance of a cell line resistant to a short term exposure to FUra (HCT-8/FU4hR) to that of a cell line resistant to a prolonged exposure to the fluoropyrimidine (HCT-8/FU7dR). Cytotoxicity studies showed that HCT-8/FU4hR cells were still sensitive to FUra given as a 7-d exposure, suggesting different mechanisms of resistance. Indeed, rapid recovery of TS activity after drug removal was evident in the HTC-8/FU7dR cell line while HCT-8/FU4hR cells were similar to the parental cell line with regard to both the degree of in situ TS inhibition by FUra and duration of inhibition after FUra removal. In contrast, labelling studies with [³H-6] FUra (4 h exposure, 100 M) showed that the incorporation of the fluoropyrimidine into RNA is significantly decreased in HCT-8/FU4hR cells as compared to parental HCT-8 cells.Given the lack of cross resistance between the two schedulesin vitro, a pilot trial was done on patients with colorectal cancer refractory to bolus FUra. On 15 patients failing after FUra+LV or FUra alone 1 PR, 3 MR, 3 SD and 8 P were observed, confirmng a certain degree of activity of CI FUra in patients clinically resistant to bolus FUra.Based on this rationale, a phase II trial of schedule-oriented biochemical modulation of FUra in advanced colorectal cancer patients was conducted, employing a hybrid regimen of 2 biweekly cycles of FUra bolus (600 mg/sqm), preceeded by (24 h interval) methotrexate, 200 mg/sqm (in order to maximize the RNA effect of the drug) alternating with FUra continuous infusion, 200 mg/sqm daily for 3 weeks, modulated by leucovorin, 20 mg/sqm weekly bolus (in order to maximize the DNA effect).Thirty-three consecutive patients (median ECOG PS 1) with advanced measurable colorectal cancer and no prior therapy for metastatic disease entered the study, from February 1992 to August 1993. Three complete and 13 partial responses were obtained among these 33 patients (RR=48%, 95% confidence limis, 31–66%). After a median follow-up time of 23 months, 16 patients are still alive. The median progression free survival and overall survival were 9.6 and 20.8 months, respectively. No toxic deaths or grade 4 toxicity occurred. The incidence of grade 3 toxicity per patient in any cycle was: mucositis 6%, diarrhea 3% and vomiting 3% for the bolus part and 21%, 3% and 6% respectively, for the continuous infusion part of the regimen. Hand-foot syndrome occurred in 27% of the patients treated with the continuous infusion regimen.In conclusion, this experimental and clinical project has generated a novel regimen of schedule oriented biochemical modulation that is twice as active and half as toxic compared to bolus FU+LV given with either the daily x 5 or the weekly schedule. This high clinical activity is very encouraging, especially considering that 1) consecutive patients were entered, 2) the responses were independently reviewed, 3) the progression free survival and survival were much longer than those actually reported for this disease, 4) the toxicity of the program, in particular the bolus regimen, was relatively low allowing further intensification.     

Analysis of the multi-stem clump structure ofLitsea japonica Juss. growing in a coastal dwarf forest

The multi-stem clump structure of a coastal dwarf forest dominated byLitsea japonica Juss. was investigated in order to clarify the sprouting characteristics and self-maintenance of clumps by stem alternation. The size and age distribution of multi-stem clumps were analyzed using cumulative relative frequency curves.L. japonica had a large number of stems and an even height distribution or young age-biased distribution of stems within a clump. These results indicated the sequential flushing of sprouts at high frequency. Height distribution within a clump ofL. japonica was relatively even compared to other species. This clump structure suggested the stable self-maintenance of individuals in all ranges of size and age without disturbances. It originated specific sprouting characteristics as a response to the severe stress of salty wind.Ardisia sieboldii Miq. had few stems within a clump. Although the stem height distribution of large individuals tended to be even, most clumps had a large size-biased distribution of stem height which indicated simultaneous sprouting. From this structure, sprouts of this species were thought to be of less significance in the stable self-maintenance of individuals thanL. Japonica.     

含金地质体表生带中主要微生物类群的研究

通过对16个含金矿区主要微生物类群的分布、生态结构的研究,发现不同类型的金矿具有不同的微生物类群.金矿矿石与金矿酸水中的自养硫细菌和异养菌分布具有明显差异,酸性水中含自养硫细菌较多,含异养菌极少;金矿氧化带中的异氧菌一般多于自氧硫细菌,其优势菌以芽孢杆菌属中蜡状芽孢杆菌为主.研究结果揭示了金矿中存在的主要微生物类群,对阐明表生金的形成、成岩和蚀变作用具有一定的意义,对发掘生物湿法冶金菌种资源具有重要作用.     

Biochemical and bioassay analysis of resistance of potato (Solanum tuberosum L.) cultivars to attack by the slug Deroceras reticulatum (Muller)

A method is described for using young field slugs Deroceras reticulatum (Muller) in a bioassay study of biochemical resistance of potato (Solanum tuberosum L.) cultivars to slugs. Tuber parts or an artificial diet were provided as food sources. Comparisons were made of feeding, survival and weight gain between the susceptible cultivar Maris Piper and the resistant cultivar Pentland Dell. Biochemical analyses were made of these two cultivars and the resistant cultivars Stormont Enterprise and Majestic. Comparisons of tuber sections and peelings as food sources indicated factors affecting growth were located in the surface layers of the tubers. Phenolics and glycoalkaloids were concentrated in the surface layers but the amounts were similar in the susceptible and resistant cultivars and the bioassays indicated that neither acting alone could explain resistance. The amounts and distribution of free amino acids also did not correlate with resistance although when supplied in the artificial diet they partly inhibited feeding. Proteinaceous inhibitors of slug gut proteolytic enzymes were present throughout the tubers but were not concentrated in the surface layers and the amounts were similar in the different cultivars thus they too did not explain the difference in susceptibility between the cultivars. Bioassays using acetone extracts (low molecular weight substances) and acetone powders (high molecular weight substances) either alone or in combination indicated that the resistant cultivar Pentland Dell contained a high molecular weight substance which together with a low molecular weight substance from either the same cultivar or the susceptible Maris Piper could confer resistance. Bioassays using protein extracts supplied in the presence or absence of chlorogenic acid indicated that this mechanism could comprise enzymic oxidation of phenolics. Assays of phenolase confirmed this since activity was highest in the outer layers of the tubers and was highest in the three resistant cultivars. Thus the chief resistance factor identified was high phenolase activity acting rapidly on phenolics when the slug first bites the tuber surface. The quantity of phenolics per se did not control the resistance. Thus while phenolics must be available, resistance is compatible with low blackening on cutting the tuber.     

Nest site choice by the three-spined stickleback, Gasterosteus aculeatus (form leiurus), in spring-fed waters

The nest site characteristics of the freshwater three-spined stickleback, Gasterosteus aculeatus (form leiurus ), were quantitatively investigated in springs and the main stream of the Yamayoke and the Tsuya River system, central Japan. Most nests (93·4%) were on a muddy or sandy substratum, at depths of 10–40 cm (84·3%), in water velocities less than 15 cm s⁻¹ (76·2%) and in the temperature range of 14 to 16° C (82·7%), Spring-fed localities provided more of these conditions than the main stream channel and hence contained more potential nesting areas. Thus, they were utilized by male sticklebacks both temporally (prolonged breeding season) and spatially (more nest sites).