Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing--a review

A widespread class of introns is characterized by a particular RNA secondary structure, based upon four conserved nucleotide sequences. Among such "class I" introns are found the majority of introns in fungal mitochondrial genes and the self-splicing intron of the large ribosomal RNA of several species of Tetrahymena. A model of the RNA secondary structure, which must underlie the self-splicing activity, is here evaluated in the light of data on 16 further introns. The main body or "core structure" of the intron always consists of the base-paired regions P3 to P9 with the associated single-stranded loops, with P2 present also in most cases. Two minority sub-classes of core structure occur, one of which is typical of introns in fungal ribosomal RNA. Introns in which the core structure is close to the 5' splice site all have an internal guide sequence (IGS) which can pair with exon sequences adjacent to the 5' and 3' splice sites to align them precisely, as proposed by Davies et al. [Nature 300 (1982) 719-724]. In these cases, the internal guide model allows us to predict correctly the exact location of splice sites. All other introns probably use other mechanisms of alignment. This analysis provides strong support for the RNA splicing model which we have developed.     

买麻藤茎的结构及其异常次生生长

买麻藤(Gnetum montanum Mgr.)茎的各类组织的排列与被子植物的茎非常相似,其次生生长也属同一类型。其中最明显的相似之处,是木质部中的导管和韧皮部中的筛分子与“伴胞”。藤本植物买麻藤,正常的次生生长开始后,由每一维管束外侧的薄壁组织经脱分化产生新的形成层,以后逐渐形成一圈维管束。这与前人所描述的新形成层来自韧皮薄壁组织是不同的。异常的维管束与正常的一样,由木质部和韧皮部组成,并被髓射线分隔呈楔形。当第一轮维管束停止生长以后,在其外围以同样方式形成新的一轮,以后并可连续形成多轮。     

STUDIES OF HAWAIIAN FRESHWATER AND SOIL ALGAE II. ALGAL COLONIZATION AND SUCCESSION ON A DATED VOLCANIC SUBSTRATE1,2

Spatial studies of colonization and succession of soil algae and chemical analyses of the various soils on the cinde cone of Kilauea Iki in Hawaii Volcanoes National Park, Hawaii are outlined. There is a positive correlation between the diversity and quantity of soil algae with nutrient levels and organic matter accumulation in each locale. Three distinct edaphic-biotic zones existing in this area are differentially revealed by the soil chemical composition, quantity and diversity of soil algae, and as evident variations in higher plant growth and colonization. Varying colonization and successional phases of higher plant growth around standing and fallen tree snags killed by volcanic activity also reflect variations in the soil algal flora. These variations appear largely as a function of differential water interception, absorption, and retention as well as differential accumulation of organic matter, and the initiation of various biogeochemical cycles.     

Periodic operation of immobilized live cell bioreactor for the production of candicidin

A lumped model for cell growth and secondary metabolite production in an immobilized live cell bioreactor has been developed. This model is applied here to simulate the performance of an immobilized bioreactor under steady-state conditions and under conditions of periodically varying concentration of a growth-limiting substrate. The results of the simulation study were experimentally verified in the case of the production of the antibiotic candicidin by Streptomyces griseus in an immobilized bioreactor with forced periodic operation. The results of the studies suggest that periodically operated immobilized live cell bioreactors can provide a potent alternative for the production of non-growth-associated biochemicals, as compared to free cell fermentations, pulsed fermentations with process cycle regeneration, and nonregenerated bioreactors. This work has demonstrated that by frequent pulsing of the growth limiting nutrient, stable extended production can be obtained at high specific cellular productivities.     

Recruitment and local persistence of a freshwater bryozoan in stream riffles

Recruitment in clonal organisms often involves both sexual and asexual processes whereby new individuals are added to adult populations. During 1988–1990,1 examined local distribution and abundance patterns, substrate colonization, and recruitment in riffle populations of the freshwater bryozoan Plumatella emarginata. Abundance levels of P. emarginata at eight selected study sites were strongly dependent on substrate size but not on overall substrate availability or stream position. Colonization of large, P. emarginata-free substrates at one site resulted in an aggregated dispersion pattern of short-lived colonies and the production of locally persistent sessoblasts. Sessoblast production rates were dependent of colony size and number. However, the estimated single season rates of colonization and recruitment were insufficient to account for the high resident population on large substrates. I conclude that sessoblast persistence is essential for escaping mortality and promoting future recruitment and local population growth and that the population dynamics of P. emarginata are strongly nonequilibrial being influenced by unpredictable disturbances as well as by rates of recruitment which increase with local density.     

Colonization of a headwater stream during three years of seasonal insecticidal applications

We investigated recolonization by insects of a small headwater stream in the southern Appalachian Mountains that was treated along its entire length with an insecticide (methoxychlor). Initial treatment (December 1985) resulted in massive insect drift. Applications continued seasonally for three years, and drift was measured during each treatment. Taxonomic composition of the drift indicated several responses: (1) Some taxa were eliminated. (2) A number of taxa occurred only sporadically following initial treatment. (3) Early instars for some taxa showed seasonal occurrences which closely paralleled known life cycles and flight periods of adults. Groups which provided strong evidence for aerial recolonization included several Ephemeroptera, Plecoptera (Peltoperlidae and Isoperla spp.), and Trichoptera (Parapsyche cardis, Diplectrona modesta, Pycnopsyche spp., and Lepidostoma spp.). (4) Some long-lived taxa survived and exhibited distinct growth through several treatment periods. These include Odonata (Lanthus and Cordulegaster), some Ephemeroptera, and some Diptera (Tipulidae, Ceratopogonidae, and Tanypodinae). (5) Some taxa which were not present at the time of initial treatment appeared during the experiment. Chironomidae dominated the drift in all samples, and the number of genera did not decrease during the three-year treatment period. Of the 27 chironomid genera identified, only Micropsectra decreased in proportional abundance during treatment. In contrast, several genera (Corynoneura, Meropelopia, Parametriocnemus, and Tvetnia) showed little change in relative abundance. Larsia (Tanypodinae) increased in proportional abundance during the treatment period.     

Evolution of mouse B1 repeats: 7SL RNA folding pattern conserved

Summary In a recent report mouse B1 genomic repeats were divided into six families representing different waves of fixation of B1 variants, consistent with the retroposition model of human Alu elements. These data are used to examine the distribution of nucleotide substitutions in individual genomic repeats with respect to family consensus sequences and to compare the minimal energy structures of the corresponding B1 RNAs. By an enzymatic approach the predicted structure of B1 RNAs is experimentally confirmed using as a model sequence an RNA of a young B1 family member transcribed in vitro by T7 RNA polymerase. B1 RNA preserves folding domains of the Alu fragment of 7SL RNA, its progenitor molecule. Our results reveal similarities among 7SL-like retroposons, human Alu, and rodent B1 repeats, and relate the evolutionary conservation of B1 family consensus sequences to selection at the RNA level.