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.     

An estimate of unique DNA sequence heterozygosity in the human genome

Summary Patients with recessive X-linked ichthyosis Patients with recessive X-linked ichthyosis (RXLI), one hereditary form of scaly skin, lack activity of the enzyme steroid sulfatase in all tissues studied. To investigate the molecular defect underlying the lack of enzyme activity, we prepared antisera against normal enzyme by injecting normal placental microsomal suspensions or partially purified steroid sulfatase into rabbits. Antibody activity was assessed by immunoprecipitation of detergent solubilized steroid sulfatase. In addition, we prepared rabbit antisera against RXLI placental microsomal suspensions. To detect immunologically cross-reactive material in patients' placentas, extracts were studied by immunoblot techniques and by competition with normal enzyme for antibody binding. Patients' extracts did not contain immunoreactive material co-migrating on electrophoresis with purified enzyme nor did they inhibit immunoprecipitation of normal enzyme. Sera from rabbits immunized with RXLI placental microsomes contain no antibodies to normal steroid sulfatase, as judged by their failure to immunoprecipitate normal enzyme or to react with normal steroid sulfatase on immunoblot. Thus the mutation in RXLI appears to reduce steroid sulfatase enzyme protein as well as enzyme activity. Portions of this material have appeared in abstract form in Clinical Research 31:564A, 1983 and 32:138A, 1984     

Primary production in Rattlesnake Springs,a cold desert spring-stream

Primary productivity and respiration were measured in Rattlesnake Springs, Washington, using the upstream-downstream diel pH-CO₂ curve and harvest methods.Daily P_g and P_n rates averaged 8.7 and 0.9, 0.6 and 0.3, and 9.3 and 1.2 g C m^–2 d^–1 for periphyton, watercress, and total community, respectively. Average photosynthetic efficiencies (%, P _n Lt^–1) were approximately 0.22 and 0.07 for periphyton and watercress, respectively. Annual community P_g was 2 700 g C m^–2 a^–1 and was highest for periphyton (2 526 g C m^–2 a^–1). Periphyton P_n (356 g C m^–2 a^–1) exceeded that of watercress (87 g C m^–2 a^–1). Community R was 2 257 g C m^–2 a^–1, and was highest for periphyton (2 170 g C m² a^–1).Desert streams appear to be enigmas in terms of their relationship between autotrophy and heterotrophy and their ability to be net importers or exporters of organic matter. The fact that they can be autotrophic and net importers of organic matter is probably related to the characteristic flash-flooding of desert streams, and emphasizes the necessity of examining these systems over more than a single annual cycle.     

Diffusion and regionalization in membranes of maturing ram spermatozoa

An essential feature of the "fluid mosaic model" (Singer, S. J., and G. L. Nicolson , 1972, Science (Wash. DC)., 175:720-731) of the cell plasma membrane is the ability of membrane lipids and proteins to diffuse laterally in the plane of the membrane. Mammalian sperm are capable of overcoming free random diffusion and restricting specific membrane components, both lipid and protein, to defined regions of the sperm's surface. The patterns of these regionalizations evolve with the processes of sperm differentiation: spermatogenesis, epididymal maturation, and capacitation. We have used the technique of fluorescence recovery after photobleaching to measure the diffusion of the lipid analogue 1,1'- dihexadecyl 3,3,3',3'- tetramethylindocarbocyanine perchlorate ( C16dil ) on the different morphological regions of testicular and ejaculated ram spermatozoa. We have found: (a) that the major morphologically distinct regions (head, midpiece, and tail) of the plasma membrane of both testicular and ejaculated spermatozoa are also physically distinct as measured by C16dil diffusibility; (b) that despite regional differences in diffusibility there is exchange of this lipid analogue by lateral diffusion between the major morphological regions of the plasma membrane; and (c) that epididymal maturation results in changes in C16dil diffusibility in the different regions of the sperm plasma membrane. In particular, the plasma membranes of the anterior and posterior heads become physically distinct.     

Histophotometric Evaluation of Glutamate Dehydrogenase Activity of the Rat Hippocampal Formation During Postnatal Development,with Special Reference to the Glutamate Transmitter Metabolism

Transmitter glutamate/aspartate synthesis is known to proceed along different metabolic pathways. In this light, the functional relevance of glutamate dehydrogenase in postnatally maturing glutamatergic/aspartatergic structures was studied by means of quantitative enzyme histochemistry. The basic requirements concerning the kinetics and calibration of the histochemical glutamate dehydrogenase reaction used were proved to be met in order to obtain valid quantitative data. The histochemically demonstrable activity of glutamate dehydrogenase (EC 1.4.1.3) in the hippocampal formation of the rat increased markedly during postnatal development. On day 30, the distribution pattern observed was similar to that in adult animals. While the enzyme activity rose within cell body layers from day 0 to day 30 by 240-285%, the increase in neuropil layers was found to be up to 830%. Maximum values were seen in the stratum lacunosum-moleculare of CA1 and CA3 and the stratum moleculare of the dentate fascia on day 30. Since the hippocampal neuropil is supposed to be copiously provided with glutamatergic (and aspartatergic?) structures which become functional in rats during the first weeks of postnatal life, the increase in enzyme activity is discussed to be primarily a consequence of maturing synaptic systems using glutamate and/or aspartate as transmitters.     

Reduced pyridine nucleotides in Pseudomonas carboxydovorans are formed by reverse electron transfer linked to proton motive force

In cell suspensions of Pseudomonas carboxydovorans pulsed with lithotrophic substrates (CO or H₂) in the presence of oxygen, formation of reduced pyridine nucleotides and of ATP could be demonstrated using the bioluminescent assay. Experiments employing base-acid transition, an uncoupler and inhibitors of ATPase or electron transport enabled us to propose a model for the formation of NAD(P)H in chemolithotrophically growing P. carboxydovorans.The protonophor FCCP (carbonly-p-trifluormethoxyphenylhydrazon) inhibited both, formation of NAD(P)H and of ATP. In the absence of oxygen, a chemical potential imposed by base-acid transition resulted in the formation of NAD(P)H and ATP when electrogenic substrates (CO or H₂) were present. This suggests proton motive force-driven NAD(P)H formation. The proton motive force was generated by oxidation of substrate, and not by ATP hydrolysis, as obvious from NAD(P)H formation during inhibition of ATP synthesis by oligomycin and N,N-dicyclohexylcarbodiimide.That the CO-born electrons are transferred via the ubiquinone 10-cytochrome b region to NADH dehydrogenase functioning in the reverse direction, was indicated by inhibition of NAD(P)H formation by HQNO (2-n-heptyl-4-hydroxyquinoline-N-oxide) and rotenone, and by resistance to antimycin A.We conclude that in P. carboxydovorans, growing with CO or H₂, electrons and a proton motive force, generated by respiration, are required to drive an reverse electron transfer for the formation of reduced pyridine nucleotides.Abbreviations CODH carbon monoxide dehydrogenase - DCCD N,N-dicyclohexylcarbodiimide - FCCP carbonyl-p-trifluormethoxyphenylhydrazon - HQNO 2-n-heptyl-4-hydroxyquinoline-N-oxide - pmf proton motive force     

Yeast pheromone alpha-factor is synthesized as a high molecular weight precursor

The sex pheromone alpha-factor of Saccharomyces cerevisiae, a tridecapeptide of approx. 1,700 molecular weight, was found to be synthesized in vivo as a high molecular weight precursor of Mr = 28,000. Inhibition of N-linked glycosylation by tunicamycin leads to three precursor species of lower molecular weight indicating three carbohydrate residues linked to the alpha-factor precursor molecule. A molecular weight of 18,000 was determined for the unglycosylated molecule.     

Convenient,laboratory procedure for producing solid d-arabino-hexos-2-ulose (d-glucosone)

The production of solid d-arabino-hexos-2-ulose (d-glucosone) from d-glucose by use of an enzyme, pyranose-2-oxidase (EC 1.1.3.10), is described. The enzyme is extracted from the mycelia of Polyporus obtusus, partially purified, and then immobilized on activated CH-Sepharose 4B. The enzymic conversion of d-glucose into d-glucosone is simple and convenient, and provides a product free from residual d-glucose. Lyophilization of the filtered reaction-solution yields the product, solid d-glucosone. Assay methods have been developed for monitoring the enzymic reaction and evaluating the purity of the final product.     

An Ultrastructural and Fluorescence Histochemical Study of the Myenteric Plexus of the Stomach of the Rainbow Trout Salmo gairdneri

The myenteric plexus of the rainbow trout Salmo gairdneri is enclosed within an incomplete Schwann-like sheath which allows bundles of unmyelinated axons to pass into the adjacent smooth muscle layers. Neuronal and non-neuronal constituents of the myenteric plexus are divided into smaller units by endoneurial collagen which in places condenses to form a perineurial covering. The myenteric plexus is avascular but arterioles and fenestrated capillaries are present close to the plexus in the intermuscular space. Small groups of neurones constitute the ganglia of the plexus but as yet few ultrastructural indications of differing neurone types have been observed. Within the neuropil of the ganglia five types of axon profile, characterised by their vesicle content, have been identified. One of these types was only recognisable following the administration of 5-hydroxydopamine. Axo-somatic and axo-dendritic synaptic contacts were only made by Type 1 axons but these were uncommon. The presence of an adrenergic component of the myenteric plexus was confirmed ultrastructually following 6-hydroxydopamine-induced degeneration and also by Falck-Hillarp fluorescence histochemistry which revealed an extensive distribution of adrenergic nerves in the plexus. The structural organisation of the plexus, the comparatively few ultrastructurally recognisable axon and neurone types and the sparsity of synaptic contacts all indicate that the teleost myenteric plexus is less complex than its mammalian counterpart.