Complete nucleotide sequence of the leader rna synthesized in vitro by vesicular stomatitis virus

The complete nucleotide sequence of the leader RNA synthesized in vitro by the Indiana serotype of vesicular stomatitis virus is presented. The sequence was determined by the technique described by Donis-Keller, Maxam and Gilbert (1977) in combination with the standard two-dimensional fingerprint techniques described by Barrell (1971). The leader RNA contains 48 nucleotides variably terminating at the 3′ terminus with cytosine (68%) and adenosine at position 47 (32%). Since the leader RNA is complementary to the 3′ terminal portion of the viral genome RNA, the first 48 nucleotides from the 3′ end of the genome RNA can be deduced. The leader RNA contains repetitive and palindromic sequences with a polypurine sequence at its 3′ terminus. The possible role of some of the sequences is discussed.     

Processing of the mouse beta-globin mRNA precursor: at least two cleavage-ligation reactions are necessary to excise the larger intervening sequence.

The β-globin mRNA precursor contains one copy of mRNA that is divided into three segments by two intervening sequences (IVS) (Smith and Lingrel, 1978; Kinniburgh, Mertz and Ross, 1978; Tilghman et al., 1978a). We have investigated the intracellular processing pathway of the 1800 nucleotide precursor by analyzing the organization of mRNA segments and intervening sequences in two classes of processing intermediates, one containing 1030 and the other 900 nucleotides. These RNAs were purified from pulse-labeled erythroid cells so that each class could be analyzed separately, thereby allowing us to derive a probable processing scheme and to compare the rates of each cleavage step. The 1030 nucleotide intermediate is 700–800 nucleotides shorter than the precursor and contains two intervening sequences. This RNA is thus generated by excision from the precursor of a major portion of the larger IVS. The 900 nucleotide RNA contains two structurally distinct molecules. One of the 900 nucleotide RNAs still contains the two IVS. The other 900 nucleotide RNA contains only one IVS derived from what was initially the larger IVS. The smaller IVS has been completely excised from this RNA to yield a spliced RNA segment derived from the 5′ terminal and middle mRNA fragments. The fully spliced 790 nucleotide β-globin mRNA is generated by excision of the remaining IVS from the 900 nucleotide RNAs. These data are consistent with a stepwise elimination of the larger IVS by at least two cleavage-ligation reactions. This result implies that the new nucleotide sequence arrangement generated by the first cleavage-ligation reaction is crucial to the precise joining of the mRNA coding regions during the final processing step.     

An approach to a physico-chemical model of olfactory stimulation in vertebrates by single compounds

During recent years, numerous attempts have been made to correlate both quantitative (Davies &; Taylor, 1959; Engen, 1962; Beck, 1964; Engen, Cain &; Rovee, 1968; Cain, 1969; Dravnieks &; Laffoit, 1970; Laffort, 1969a,b) and qualitative (Davies, 1965; Amoore &; Venstrom, 1965; Döving, 1966a,b; Wright &; Michels, 1964; Leveteau &; MacLeod, 1969) odorous properties of single compounds to their molecular properties. These attempts have been only partially successful.In the present paper we will try to explain the several odorous properties of single compounds on the basis of the non-specific properties of odorants involved in solubility.This model is a first approach, and although it gives statistically highly significant relations, it is not as accurate as those advanced with respect to the physical and sensory dimensions of stimuli in the fields of vision and audition.We will first give the present definitions of the most suitable physicochemical parameters, and then advance quantitative and qualitative models for single compounds. Quantitative odorous properties are: odour threshold, rate of change of odour intensity with odorant concentration in the suprathreshold region, and the somewhat controversial upper odour intensity. Qualitative properties refer to odour character.     

Replication of polyoma DNA in isolated nuclei. VII. Initiator RNA synthesis during nucleotide depletion.

Earlier experiments demonstrated that the Okazaki fragments synthesized during discontinuous polyoma DNA synthesis in isolated nuclei at their 5′ ends contained structural elements consisting of polyribonucleotides starting with ATP or GTP (Reichard et al., 1974). These structures could be released by digestion with pancreatic DNAase and were named initiator RNA. They consist of a large family of polyribonucleotides differing in base sequence but having a common size of about a decanucleotide. We now demonstrate that limitation of DNA synthesis by low concentrations of deoxyribonucleoside triphosphates in parallel limits the synthesis of initiator RNA. This is additional evidence for the primer function of initiator RNA. When ribonucleoside triphosphates other than ATP were deleted from the incubation medium only a small decrease of DNA and initiator RNA synthesis occurred. Under those conditions deoxyribonucleotides substituted for ribonucleotides and were incorporated internally into the primer. From this result as well as the insensitivity of initiator RNA synthesis to α-amanitin (Reichard &; Eliasson, 1979) we suggest that a mammalian counterpart to primase, the dnaG gene product of Escherichia coli(Rowen &; Kornberg, 1978a), catalyzes the synthesis of initiator RNA.     

Theory of radiation dose-survival curves for the case where organism lethality is defined as loss of reproductive capacity. II. Application to cells and physical interpretation

The general theory of survival curves (Craig, 1971) is applied to the case of cells and sub-cellular organisms with a physical interpretation via gene or chromosome damage as the terminal lesion.It is indicated how the proposed terminal lesion is consistent with the salient features of cellular response to radiation and analytical expressions for reactivity and sensitivity in terms of a damage, or mutation, cross section are obtained.The probability of a complex cross section and conditions under which it reduces to simple approximations are discussed and the influence of various factors on the cross section are indicated.Acceptable fits are obtained to the data of Barendsen, Beusker, Vergroesen &; Budke (1960), McCulloch &; Till (1962) and Puck &; Marcus (1956) with simple forms of cross section.     

Sequence from the assembly nucleation region of TMV RNA

In an effort to isolate RNA sequences containing the assembly nucleation region, uniformly ³²P-labeled tobacco mosaic virus RNA was partially digested with pancreatic ribonuclease, and the mixture of fragments was incubated with limited amounts of tobacco mosaic virus protein disks in conditions favorable for reconstitution. The RNA fragments which became encapsidated were purified and sequenced by conventional techniques. The sequence of the first 139 nucleotides of P1, the principal encapsidated fragment, is AGGU- UUGAGAGAGAAGAUUACAAGCGUGAGAGACG- GAGGGCCCAUGGAACUUACAGAAGAAGUUGU- UGAUGAGUUCAUGGAAGAUGUCCCUAUGUCA- AUCAGACUUGCAAAGUUUCGAUCUCGAACCG- GAAAAAAGAGU. Residues 1–110 of P1 overlap the assembly origin isolated and characterized in the accompanying papers by Zimmern 1977 and Zimmern and Butler 1977. Our results, taken in conjunction with the two accompanying papers, define the sequence of much of the nucleation region as well as sequences flanking it on both sides. The features of the P1 sequence which may have a role in the nucleation reaction are discussed in detail in the text.     

The role of migration in the genetic structure of populations in temporally and spatially varying environments II. Island Models

The Island Model introduced by Sewall Wright (1951) has proven to be a useful construction for studying the interaction of genetic drift, population subdivision, and mutation. Interest in the model has recently increased because of its relevance to certain questions involving the rate of differentiation of sub-populations under the neutral allele hypothesis (e.g., Smith, 1970; Latter, 1973). It is perhaps the only realistic population structure in which the test for neutrality proposed by Lewontin and Krakauer (1973) is valid (Lewontin and Krakauer, 1975). If data from natural populations is to be compared to the predictions of the Island Model, it is desirable to have an alternative model with the same migration pattern but with natural selection operating. In this paper one such model will be introduced where the stochastic element comes from random fluctuations in the environment rather than from genetic drift. The model is a direct extension of the one in the previous paper in this series (Gillespie, 1975) which dealt with a population which is subdivided into two patches with restricted migration between them.     

Kinship and covariance

Price's (1970) covariance theorem can be used to derive an expression for gene frequency change in kin selection models in which the fitness effect of an act is independent of the genotype of the recipient. This expression defines a coefficient of relatedness which subsumes r(Wright, 1922), b(Hamilton, 1972), ρ (Orlove &; Wood, 1978), and R(Michod &; Hamilton, 1980). The new coefficient extends the domain of Hamilton's rule to models in which the average gene frequency of actors differs from that of recipients.     

Mitochondrial RNAs are abundant in the poly(A)+RNA population of early frog embryos

Mitochondrial sequences have been identified within a set of cloned complementary DNAs that had been copied from poly(A)⁺RNA of two embryonic stages of Xenopus laevis (Dworkin and Dawid, 1980, Dworkin and Dawid, 1980, Develop. Biol.76, 435–448 and 449–464). Mitochondrial sequences were found to be highly abundant in gastrula stage poly(A)⁺RNA sequences; in tadpole RNA their relative abundance is reduced severalfold. Mitochondrial sequences account for the most abundant poly(A)⁺RNA molecules in the gastrula population. The high abundance of mitochondrial RNA in early stages may be the consequence of the accumulation of large numbers of mitochondria in the egg.     

Selective resistance of bacterial polyadenylate-containing RNA to hydrolysis by guanosine 3'-5'-monophosphate-sensitive nuclease of Bacillus brevis

Earlier experiments had shown that the degradation of newly synthesized RNA in permeable cells of Bacillus brevis is mediated primarily by a guanosine 3′,5′-monophosphate-sensitive 3′-exonuclease [N. Sarkar and H. Paulus (1975) J. Biol. Chem. 250, 684–690]. More recently, we found that a substantial fraction of pulse-labeled RNA in B. brevis is polyadenylylated [N. Sarkar, D. Langley, and H. Paulus (1978) Biochemistry 17, 3468–3474], and it was thus of interest to examine the effect of polyadenylylation on the susceptibility of RNA to degradation by the 3′-exonuclease. Purified 3′-exonuclease from B. brevis hydrolyzed the unadenylylated fraction of pulse-labeled RNA from B. brevis much more rapidly than poly(A)-containing RNA. Similar results were obtained with the pulse-labeled unadenylylated and polyadenylylated RNA fractions from Bacillus subtilis. Control experiments showed that the differential hydrolysis of the labeled RNA preparations by 3′-exonuclease was not due to the presence of inhibitors or activators. These results suggest that the stability of mRNA in Bacillus species may be regulated by polyadenylylation.     

The fine structure of Ameson pulvis (Microspora,Microsporida) and its implications regarding classification and chromosome cycle

Nosema pulvisPerez, 1905, Ameson pulvis (Perez) Sprague, 1977, in muscles of the crabs Carcinus maenas and C. mediterraneus from the coast of France, was observed with the electron microscope. It was found to be structurally similar to the type species A. michaelis (Sprague, 1970). Sprague, 1977, having moniliform sporogonial plasmodia, unikaryotic sporoblasts, and hirsute sporulation stages. It is treated as distinct from A. michaelis because it has slightly smaller spores (by comparison with syntype material of A. michaelis) and appears to have fewer coils in the polar filament. The results require the removal of the genus Ameson from the family Nosematidae Labbé, 1899, where Sprague (1977) had placed it under the erroneous supposition that its sporoblasts are diplokaryotic. Ameson is transferred to family Unikaryonidae Sprague, 1977. Ameson is distinguished from PereziaLéger and Duboscq, 1909, shown by Ormieres et al. to have a similar developmental pattern, by presence of appendages on its sporulation stage. A. nelsoni (Sprague, 1950), the third, and only other species of Ameson, lacks the appendages and is transferred to genus Perezia.     

Box-Jenkins forecasting in ecology: An answer to poole

This answering of Poole, 1978, Poole, 1976 aims at rounding off our exchange of views, without losing the readership from an excess of toing and froing between the four contributions. So my final rejoinder only attempts at treating the general points raised by Poole (1978), rather than taking issue with all the minutiae, which would require too many quotes of quotes and counterquotes. The main nub of contention remains as to whether or not statistical fits can be meaningfully interpreted biologically.     

Complexity-stability relationship of two-prey-one-predator species system model: Local and global stability

Parrish & Saila (1970), motivated by the experiments of Paine (1966), constructed a simple mathematical model for a two-prey-one-predator system. They were unable to find, in their model, a set of parametric values with which the three-species system can be stable, whereas a twoprey species system without a predator is unstable. Cramer & May (1972) showed that, in fact, such parametric values exist, and gave the necessary mathematical condition. I have investigated the complete conditions for the stability of the system around the equilibrium point, and show that the conditions must be more stringent than given by Cramer & May (1972). Also, it is shown that the present model can have a globally stable limit cycle in three species even when the equilibrium point is locally unstable.     

Does a functional relationship exist between the polymerization and catalytic activity of beef liver glutamate dehydrogenase?

The recent work of Cohen &; Benedek (1976) and Cohen et al. (1975, 1976) on the apparent interdependence of beef liver glutamate dohydrogenase catalytic activity and degree of polymerization is examined in the light of previously published equilibrium and kinetic results. It is shown that some of the hypotheses central to the Cohen &; Benedek (1976) model are in contradiction with existent data. Consideration of all available information leads to the conclusion that effector-induced depolymerization may simply be an incidental side reaction in the events leading to inhibition.     

Trehalose-6-phosphate synthetase activity in extracts of Dictyostelium discoideum.

Trehalose-6-phosphate (T-6-P) synthetase activity in extracts of Dictyostelium discoideum has been reexamined in an effort to resolve discrepancies between the results of previous studies (R. Roth and M. Sussman (1966). Biochim. Biophys. Acta, 122, 225; K. A. Killick and B. E. Wright (1972). J. Biol. Chem., 247, 2967). We find that T-6-P synthetase is not cold sensitive as reported by Killick and Wright (1972), is not present in bacterial-grown vegetative cells (though subject to some modulation by other nutritional conditions), and is not in our hands unmasked or activated by ammonium sulfate fractionation. We conclude that the pattern of T-6-P synthetase accumulation and disappearance during fruiting body construction in D. discoideum is as originally described by R. Roth and M. Sussman (1968). J. Biol. Chem., 243, 5081) and confirmed elsewhere (P. C. Newell et al. (1972). J. Mol. Biol., 63, 373; R. W. Brackenbury et al. (1974). J. Mol. Biol., 90, 529; B. D. Hames and J. M. Ashworth (1974). Biochem. J., 142, 301).