A microcomputer program for the identification of tRNA genes

A microcomputer program which locates tRNA genes within longDNA sequences is described. The search is performed either byidentifying tRNA-like secondary structures or by locating eukaryoticRNA polymerase III promoter consensus sequences. The programis also useful in finding inverted repeats allowing the formationof stem-loop secondary structures in tRNA. The program has beendeveloped in BASIC and 6502 Assembler and runs on the AppleII plus and He microcomputers. The execution is quite fast;all the operations are carried out in 1–90 s, dependingon the required task and on the sequence length. Received on March 1, 1985; accepted on April 25, 1985     

A general purpose non-linear curve fitting program for the British Broadcasting Corporation Microcomputer

Software for non–linear curve fitting has been writtenin BASIC to execute on the British Broadcasting CorporationMicrocomputer. The program uses the direct search algorithmPattern–search, a robust algorithm that has the additionaladvantage of needing specification of the Junction without inclusionof the partial derivatives. Although less efficient than gradientmethods, the program can be readily configured to solve low–dimensionaloptimization problems that are normally encountered in lifesciences. In writing the software, emphasis has been placedupon the ‘user interface’ and making the most efficientuse of the facilities provided by the minimal configurationof this system. Received on March 4, 1985; accepted on March 14, 1985     

Optimal alignments of biological sequences on a microcomputer

An algorithm and a program have been developed which enableoptimal alignments of biological sequences on an 8–bitmicrocomputer. The compiled program can process sequences upto 1000 residues on a Commodore 64. Since this program was writtenoriginally in the BASIC language, it may readily be adaptedto other microcomputers with small changes. Received on March 11, 1985; accepted on March 14, 1985     

Computer program for prediction of the optimal and suboptimal secondary structures of long RNA molecules

We present an algorithm for prediction of RNA secondary structures.The program consists of three parts: the first computes locationand free energy of every possible stem–loop structure,the second computes probability of its formation, and the thirdlists the positions and free energies of all the stem–loopsin the order of their probability sizes. The circular RNA moleculeof chrysanthemum stunt viroid was used as an input data fordemonstrating the operation of the program. Received on March 14, 1985; accepted on March 18, 1985     

REPRODUCTIVE CYCLES OF CERASTODERMA GLAUCUM(BRUGUIERE) AND C. EDULE (L.) WITH SPECIAL REFERENCE TO THE EFFECTS OF THE 1981-82 SEVERE WINTER

Gonadal changes in two species of Cerastoderma occurring indiscrete populations in South Wales were monitored by stereologicalanalysis during the breeding seasons of 1981 and 1982. Fecundityand spawning efficiencies were determined quantitatively. Therelationship between reproductive activity and changes in meatcondition are discussed. Both species are opportunistic breeders. Their normal patternsof reproduction are similar, consisting of minimum activityin winter and peak activity during spring/early summer. Thetwo species were affected differently by the severe winter of1981–82—C. glau-cum exhibited a single, ‘epidemic’spawning and resumed gametogenesis after a 4-month resting period.C. edule adopted a ‘polycyclic’ pattern withouta resting period. Both of these unusual reproductive strategies,augmented by reduced predation resulted in heavy spatfalls. (Received 20 March 1985; revised 20 March 1985;     

A new method for finding long consensus patterns in nucleic acid sequences

We describe a fast computer algorithm for identifying consensuspatterns in DNA sequences. The method requires no prior assumptionsabout the consensus pattern other than its length. In particularno previous knowledge of the frequency or spacing of consensuspatterns is required. However, a priori information about theshape of the consensus pattern, or invariability of individualpositions, or the overall conservation level, can be utilizedto enhance the selectivity and sensitivity of search. As thenumber of all possible consensus words increases very rapidlywith length, comprehensive searches have usually been restrictedto a maximum of 10–12 nucleotides, even when large mainframesare used. Our algorithm enables searching for consensus patternsof this order on current mid-range and powerful microcomputers.Searches may be conducted on single, long sequences or a setof possibly aligned shorter sequences. We give examples of identifiedconsensus patterns in both prokaryotic and eukaryotic DNA sequences,along with some typical program timings. Received on January 14, 1991; accepted on March 5, 1991     

Phytoplankton studies in the fjords of West Spitzbergen: physical environment and production in spring and summer

The phytoplankton in the fjords of West Spitzbergen was investigatedfrom 1978 to 1985. The spring bloom lasted longer than at theNorwegian coast: from mid March to early June. There is no delayin the onset of the spring bloom in Spitzerbergen fjords relativeto fjords of northern Norway. This is probably related to therapid daylength increase at high latitudes. The phytoplanktonspecies composition during spring was comparable to that alongthe coast of northern Norway. Annual primary production in theinvestigated area was calculated to be 150 g C m^–2 year^–1.     

Records and life history of Praunus flexuosus (Crustacea: Mysidacea) in Icelandic waters

Since its fust record in Icelandic waters in 1970, Praunus flexuosushas been found to be very common in the littoral zone of theAtlantic water at the south-west coast of Iceland. It seemspossible that P. flexuosus has only recently been introducedinto Icelandic waters. The life history of P. flexuosus hasbeen followed in Skerjafjord, near Reykjavik, in 1985–1986.The animals have a one-year life span. The females, some ofwhich appear to produce three broods, breed mainly during June–August.Breeding females ranged in length from 18.7 to 25.7 mm and thelargest brood was 72 eggs. The incubation time at c. 11°Cwas estimated to be 25 days. The daily growth rate of juvenileswas estimated to be 0.16 mm in July–August and 0.05–0.07mm in September–October. No growth occurred during thewinter months of October–March.     

Selective Iodo-Labeling of an Intrinsic Electron Donor of Photosystem II in Illuminated Tris-Treated Thylakoids

Peptides that participate in the oxidizing side of PS II wereselectively tagged with iodine, activated by illuminated Tris-treatedthylakoids. A peptide of 29 kDa was iodinated, with less labelingof 33- and 58-kDa peptides. The iodination was inhibited byDCMU, and suppressed when the Tris-treated thylakoids were supportedby diphenylcarbazide. No peptide in the untreated thylakoidswas iodinated. These findings indicate that the oxidation ofI^– at the oxidizing side of photosystem II results iniodination. The iodinated peptide of 29 kDa was identified to be one ofthe major components of the isolated PS II reaction center complexfrom the following characteristics of the peptide: 1) polymerizationon heat-treatment (95C, 5 min) of the iodinatcd thylakoidsin the presence of SDS and 2-mercaptoethanol, 2) thylakoid-bindingafter NaSCN-washing, and 3) migration distinct from that ofthe herbicide-binding protein in SDS-polyacrylamide gel electrophoresis.Thus, the iodinated 29-kDa peptide is a secondary electron donorof PS II or the nearest one to a site where I^– is oxidized. (Received March 13, 1985; Accepted June 5, 1985)     

Studies of Growth and Flowering in Picea sitchensis (Bong.) Carr. 2. Initiation and Development of Male, Female and Vegetative Buds

Vegetative shoots from the base of the crown, and from partsof the tree likely to form male or female buds, were collectedfrom 40–years–old trees of Picea sitchensis (Bong.)Carr. throughout the 1973–4 annual growth cycle. The morphologyand growth rates of the terminal buds on these shoots were assessed. Bud scale primordia were formed most quickly in the female position,at an intermediate rate in the male position and most slowlyin the basal vegetative position during April, May and June.In July and early August the apical meristems swelled to formdomes and continued to grow at the same relative rates in themale, female and basal vegetative positions. Reproductive budswere first morphologically distinct in late August and sporangiaappeared in October. Dormancy, defined by the pause in apicalvolume increase, extended from mid-October to mid–March.Young strobili grew much faster than basal vegetative shootsof the same age between mid–March and bud burst in lateApril. Throughout the growth cycle, external changes in budsize reflected changes in size of the apical meristem, youngstrobihis or young vegetative shoot inside the bud. It is proposed that the rate of growth of an apical meristemmay be causally related to the type of bud which subsequentlydevelops from it. Sitka spruce, Picea sitchensis, bud development, morphology, growth of apical dome, flowering     

Microcomputer tools for steady-state enzyme kinetics

Three programs useful for the investigation of steady–statekinetics have been developed. Two provide the solution to thesteady–state rate equation; the first of these is a straightforwardimplementation of the rules developed by Chou. The second isa very efficient procedure for evaluating King–Altmandiagrams and can be used for quite large mechanisms. The thirdprogram provides the numeric solution for a specific mechanismand set of initial conditions; it is well suited to extremelylarge models. Received on April 1, 1985; accepted on April 19, 1985     

Conductometric Method for Detecting Ion Efflux during a Single Action Potential of Chara

A simple device was developed to detect net ion efflux duringa single action potential of Chara as an increase in the electricconductance of the bathing solution. The device showed a sufficientlyhigh sensitivity and rapid response to the increase in the electricconductance. Net efflux of monovalent ions was estimated as65–660 pmol cm^–2 impluse^–1 (average 220 pmolcm^–2 impulse^–1). (Received June 28, 1985; Accepted November 13, 1985)     

Temporal Changes in Swimming Direction during the Phototactic Orientation of Individual Cells in Cryptomonas sp.

The response of individual Cryptomonas cells to continuous lightwas recorded using infrared video-micrography. Swimming directionsand temporal shifts in swimming direction of each cell weremeasured. White light of 0.1–1 W m^–2 elicited apositive phototactic orientation, but did not induce any photophobicresponse. Light of 100 W m^–2 induced a photophobic responseat the onset of actinic irradiation, but did not induce positivephototactic orientation. No correlation between positive phototacticorientation and photophobic response was found in this species.The direction toward the light source was defined as 0°,and the direction away from the source as 180°. Within 2s after the onset of lateral monochromatic light of 570 nm at0.1 W m^–2, cells which were swimming in a direction ofless than 120° predominantly shifted their course towardthe light source. Cells swimming in directions of larger than120° shifted their course as randomly as those in the dark.Thus, for phototactic orientation, the cells must perceive thelight from their anterior side. (Received July 29, 1985; Accepted November 4, 1985)     

Accurate and Simple Measurement of Phytic Acid Contents in Cereal Grains

We developed an accurate and simple method for measuring thephytic acid contents in cereal grains on the basis of closeexamination of various factors affecting the accuracy and reproducibilityof the measurement. Our conclusions were: (1) As extracting medium for phytic acid,HCl was better than trichloroacetic acid or H₂SO₄. (2) The suitablepH range for extracting phytic acid was 0.3 to 1.0. (3) Completeformation of Fe-phytate required four to nine times as muchFe^3$ as phytic acid. (4) No definite effect of Na₂SO₄ on therecovery of phytic acid was observed, though it increased theextracting efficiency of trichloroacetic acid. (5) The determinationlimit of phytic acid by the iron precipitation method was 3.3µmol per 20 ml. Our new method gave reliable results, and a linear relationshipof y=0.3163x$0.0597 was obtained up to 0.025 µmol µ^–1between the concentration of phytic acid and the zone lengthin isotachophoresis. The phytic acid contents of two kinds ofrice, two kinds of rye, and one kind of wheat and of barleywere determined with this method. (Received March 19, 1985; Accepted August 2, 1985)     

Particulate and dissolved phytoplankton production of the Patos Lagoon estuary, southern Brazil: comparison of methods and influencing factors

Uptake rates of ¹⁴C (filtration and the acidification-bubblingmethod—ABM) were measured weekly in a shallow region ofthe Patos Lagoon estuary (3207'S, 5206'W) between March 1989and March 1990. Phytoplankton production varied seasonally,the lowest values occurring in the austral winter (June–August1989) and the highest rates during spring and summer (March1989; September 1989–March 1990). Particulate carbon productionvaried between 0.65 and 70.6 mg C m^–3 h^–1 and wasmostly associated with organisms <20 µm (mean = 73.4%).Dissolved organic carbon (DOC) released by phytoplankton variedbetween 0.1 and 89.3 mg C m^–3 h^–1 representing     

Biosynthesis of folic acid compounds in plants VI. The occurrence and properties of the dihydrofolate-synthesizing enzyme in pea seedlings

An enzyme, which catalyzes the formation of dihydrofolate fromdihydropteroic acid and L-glutamic acid, was found in pea seedlings.The enzyme was purified approximately 25-fold from the crudeextracts of pea seedlings, and its some properties were investigated.Optimum pH for the enzyme activity was found to be 8.8. Pteroicand tetrahydropteroic acids were not active as substrate. Theenzymatic reaction required as cofactors ATP, divalent (Mg²⁺or Mn²⁺) and univalent (K⁺, NH₄⁺ or Rb⁺) cations. The productwas characterized as dihydrofolic acid by bioautography. MICHAELIS constants for L-glutamic acid, ATP, dihydropteroicacid and Mg²⁺ were 7.0x10^–4, 9.0x10^–5, 3.5x10^–6and 1.2x10^–3 M, respectively. The MICHAELIS constant forMn²⁺ was 3.0x10^–4. The enzyme was inhibited by PCMB orsilver nitrate and, to some extent, by L-aspartic acid. Inhibitionby PCMB was completely reversed by addition of 2-mercaptoethanol.Enzyme activity was distributed widely among plants. The importanceof magnesium and potassium ions for enzyme catalysis is discussed. ¹For the previous paper, Part V, see Reference (30). (Received March 28, 1970; )     

Influence of Chlorocholine Chloride on Grain Growth of Winter Barley (Hordeum distichon L. cv. Igri) in the Field

Green, C. F., Dawkins, T. C. K. and McDonald, H. G. 1985. Influenceof chlorocholine chloride on grain growth of winter barley (Hordeumdistichon L. cv. Igri) in the field.–J. exp. Bot. 36:1126–1133. Chlorocholine chloride was applied to winter barley either inthe Spring or Autumn. It increased grain number per unit croparea. Rates of incorporation of dry matter into the grain weredecreased, but the period of growth was extended by the treatments.Overall the final mean grain weight was reduced so that no advantagesin terms of yield resulted from the increased grain numbers. Key words: —Chlormequat, chlorocholine chloride, CCC, Hordeum distichon L., barley, grain growth, grain weight, senescence, grain yield     

Redistribution of Phosphorus, Sulfur, Potassium and Calcium in Relation to Light-Induced Gravitropic Curvature in Zea Roots

Phosphorus, sulfur, potassium and calcium were measured by particle-inducedX-ray emission (PIXE) in horizontally oriented, light-irradiatedor non-irradiated primary roots of Zea mays L., cv. Golden CrossBantam 70 which exhibit gravitropic response only after exposureto light. The content of the four elements increased in thelower half of horizontally oriented roots which had been brieflyexposed to white or red light, while there were no marked differencesin distribution between the upper and lower halves of non-irradiatedroots. The increase of each element in the lower half was observed15–30 min after irradiation in root caps and 30–60min after irradiation in the elongation zones. The effect ofred light was not reversed by far-red light given immediatelyafter the red irradiation. Ethylene glycol-bis(ß-aminoethylether)-N, N, N',N'-tetraacetic acid (EGTA) treatment of roottips inhibited the gravitropic curvature of roots, and the additionof Ca reduced this inhibition. The meaning of Ca redistributionin root caps and elongation zones during light-induced gravitropiccurvature of maize roots is discussed. (Received December 4, 1985; Accepted March 22, 1986)     

The Role of Maturation Drying in the Transition from Seed Development to Germination: II. POST-GERMINATIVE ENZYME PRODUCTION AND SOLUBLE PROTEIN SYNTHETIC PATTERN CHANGES WITHIN THE ENDOSPERM OF Ricinus communis L. SEEDS

Kermode, A. R. and Bewley, J. D. 1985. The role of maturationdrying in the transition from seed development to germination.II. Post–germinative enzyme production and soluble proteinsynthetic pattern changes within the endosperm of Ricinus communisL. seeds.—J. exp. Bot. 36: 1916–1927. Immature seedsof Ricinus communis L. cv. Hale (castor bean) removed from thecapsule at 30 or 40 d after pollination (DAP) do not germinateunless first subjected to a desiccation treatment. This changefrom development to germination elicited by premature desiccationis also mirrored by a change, upon subsequent rehydration, inthe pattern of soluble protein synthesis within the endospermstorage tissue. Following rehydration of prematurely dried 30or 40 DAP seeds, soluble proteins characteristic of developmentcease to be synthesized after 5 h of imbibition, and those uniquelyassociated with germination and growth are then produced. Apattern of soluble storage protein breakdown comparable to thatfound in endosperms from mature seeds following imbibition isalso observed. In contrast, hydration of 40 DAP seeds immediatelyfollowing detachment from the mother plant results in a continuationof the developmental pattern of protein synthesis. Prematuredesiccation at 40 DAP elicits the production within the endospermof enzymes involved in protein reserve breakdown (leucyl ß–naphthylamidase;LeuNAase) and lipid utilization (isocitrate lyase; ICL) to levelscomparable to those observed in mature–hydrated endosperms.It is proposed that drying plays a role in redirecting metabolismfrom a developmental to a germinative mode; it also appearsto be a prerequisite for the induction of hydrolytic enzymesessential to the post–germinative (growth) phase of seedlingdevelopment. Key words: Desiccation-tolerance, germinability, seed development, castor bean     

Enhancement of Oxygen-Evolution in Photosystem II-Phycobilisome Particles from Porphyridium cruentum

Oxygen-evolving photosystem II-phycobilisome particles froma red alga were inhibited 50–80% by aging, dilution, lowpH and salt-washing. Bovine serum albumin, and dithiothreitolwere found to stimulate activity in all but salt-washed particles.CaCl₂ and MnCl₂ partially restored activity lost after agingor dilution. ¹Current address: Waksman Institute of Microbiology, RutgersUniversity, Piscataway, New Jersey 08854-0759, U.S.A. (Received October 5, 1985; Accepted March 31, 1986)