Phylogenetic comparative analysis of RNA structure on Macintosh computers

A Macintosh Hypertalk program (Hypercard ‘stack’)for use in phylogenetic comparative analysis of RNA structureis described. The program identifies covariations and compensatorychanges in RNA sequence alignments, for use in the constructionof secondary structure models or the identification of tertiaryinteractions. The results of an analysis are presented eitheras a list of positions in the alignment which covary, or asa 2-dimensional matrix in which potential helices in the secondarystructure appear as diagonal patterns. Received on January 7, 1991; accepted on March 19, 1991     

Mapping DNA by stochastic relaxation: a new approach to fragment sizes

Instead of the traditional manipulations with given fixed fragmentlengths in the restriction map construction a method of varyingthe lengths is proposed and realized under the simulated annealingalgorithm scheme. The described approach has no upper limiton the number of fragments mapped with even ordinary hardware.A program has been derived from the algorithm combined withthe least–squares refinement procedure for both linearand circular maps. The algorithm's abilily to pick up missedmaps is illustrated and the problem of reducing the number ofsolutions is discussed. Received on January 8, 1990; accepted on January 9, 1990     

Picoplankton dynamics in Davies Reef lagoon, the Great Barrier Reef, Australia

The diel variations in abundance and frequency of dividing cells(FDC) of coccoid cyanobacteria in a coral reef lagoon were investigatedin June, September and December 1989, and April 1990. Cyanobacteriaand picoplanktonic eukaryotes (<3 µm) were sampledmonthly from January to December 1990. The average abundancesof cyanobacteria and eukaryotes ranged between 1.17–10.0610⁴cells ml^–1 and 0.16–2.4110⁴ cells ml^–1, respectively,with abundances of both being higher in summer (November-April)than in winter (May-October). The ratio of cyanobacteria toeukaryotes fluctuated from 1.93 to 8.67, independent of theseasonal variation in their abundances. The instantaneous growthrate of cyanobacteria, which was estimated from the daytimeabundance increment, ranged between 0.430 and 3.144 day^–1The estimated daily specific growth rate of cyanobacteria bythe FDC method ranged between 0.231 and 0.966 day^–1. InApril, despite the high specific growth rate and low flushingconditions. cyanobacterial abundance showed a cyclic diel pattern,suggesting a strong grazing impact on their population.     

MANSEK and SUNHCA. Two interactive programs for the hydrophobic cluster analysis of protein sequences

Hydrophobic cluster analysis (HCA) is an efficient method foranalysing and comparing the amino acid sequences of proteins.It relies on two–dimensional representations of the sequencespresently generated by simple plot programs working on microcomputers.Two interactive programs, MANSEK. and SUNHCA, are describedhere that operate from Vax and Sun workstations respectively.These programs allow the display of several protein sequencesin the form of two–dimensional helical plots suitablefor HCA. Several tedious, repetitive and timeconsuming stepsof HCA have been suppressed by implementing several featuressuch as interactive on–screen manipulations (zoom, translations)of the plots and HCA score calculations on segments chosen bythe user. Plots on paper can be obtained through hard copiesor plotting subroutines.     

Light Inhibits Flagellation in a Chlamydomonas Mutant

We have isolated a new flagellar mutant in Chlamydomonas reinhardtii.When the mutant was cultured under the white fluorescent lamp({small tilde}4,800 lux), most cells had no flagella. However,when the cultures were put in the dark, flagellation occurred.Greater than 70% of the cells had flagella within 12–16h after the transfer. The flagellar morphology varied from "rod-shape"(same as the wild-type flagella) to "disk-shape". The disk-shapedflagella had the axonemes which were curved into a loop withinthe swollen membrane. Hence, this mutant is called loop-1. Light-inhibitionof flagellation was restored in the presence of 10^–5 MDCMU. The spectral dependency of the photo-inhibition of flagellation,determined using the Okazaki Large Spectrograph, showed maximaleffectiveness at 400–420 nm and 600–680 nm. Theseresults suggest that photosynthesis inhibits flagellation ofloop-1 cells. (Received July 27, 1989; Accepted January 29, 1990)     

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     

Seasonal occurrence and vertical distribution of appendicularians in Toyama Bay, southern Japan Sea

To investigate seasonal variation in the community structureof appendicularians, vertical hauls (0–500 m) with a Norpacnet were made at an offshore station in Toyama Bay at intervalsof 2–4 weeks from February 1990 to January 1991. Additionalsamples were collected with MTD nets at 12–17 differentdepth layers between the surface and a depth of 600–700m at the same position in June, September and December 1986,and March 1992, to examine the vertical distribution of appendicularians.Twenty-one species (including two unidentified species) belongingto five genera were found, and the dominant species were dividedinto three groups by their occurrence period. Oikopleura longicauda,Fritillaria borealis f. typica and F. borealis f. sargassi occurredthroughout most of the year. Fritillaria pellucida, O. fusiformisand O. rufescens were found in summer and autumn. Oikopleuradioica was found in spring and winter. Oikopleura longicaudawas overwhelmingly the most abundant species throughout theyear. This species was always distributed in the upper 100 mdepth, with a peak at a depth of 0–50 m that correspondedto the peak of chlorophyll a concentration during the day andnight in all seasons. The day–night vertical distributionpatterns of F. borealis f. typica, F. pellucida, O. fusiformisand O. rufescens were similar to that of O. longicauda. Seasonalvariations in abundance of appendicularians are considered tobe the result of biological factors rather than physical factorssuch as temperature and salinity. In particular, O. dioica seemsto be affected by food availability.     

Mortality and Self-thinning in Postfire Black Spruce

Using age-structure determinations on both living and dead stemsin censused plots, coupled with stem analysis techniques, anhistorical picture of mortality and above-ground tree stem growthwas recreated for ten stands dominated by black spruce in northeasternOntario, Canada. No evidence of mortality was seen in any plot prior to 30 yearsfollowing postfire initiation. Each of the eight oldest standsshowed a linear decline in numbers for a 20–25 year period.The steepness of the mortality slope was proportional to initiallive stem density within and among plots during this phase.The final 10–20 years was marked by a less steep declinein numbers. The log density vs log mean tree volume curves in the eightoldest stands were doubly asymptotic and were fitted to a logisticcurve very tightly in each case. At the point of inflectionthe curves' slopes ranged from –2.14 to –3.89. However,log density vs log mean stem volume among stands at this pointof inflection had a slope of –0.96. Reasons for the inconsistency between within-stand and among-standself-thinning estimates are considered, as well as the poorfit to the –3/2 rule. Ecosystem processes related to thechange in nutrient relations during stand growth are identifiedas a prime influence on self-thinning behaviour in natural blackspruce stands. Mortality, stem analysis, self-thinning, Picea mariana, black spruce     

Variations in Lipid and Fatty Acid Content in Relation to Acetyl CoA Carboxylase in the Marine Prymnesiophyte Isochrysis galbana

Lipid and fatty acid content was determined in Isochrysis galbanacultures grown under various environmental conditions in steadystate continuous cultures. Lipid and fatty acid accumulationwas observed under severe nitrogen limiting conditions. Therate of in situ lipid synthesis, determined from ¹⁴C bicarbonateincorporation into lipid fraction, decreased under nitrogenlimited growth (µ<0.72day^–1), concomitant witha reduction in the in vitro activity of the enzyme acetyl CoAcarboxylase. Cellular lipid and fatty acid content remainedfairly constant over a wide range of irradiance levels. Therate of lipid synthesis, however, increased as irra-diance levelwas elevated to a maximal value at a light intensity of 150µmolquanta m^–2s^–1 and slightly decreased at a higherphoton flux. The in vitro activity of ACCase roughly followedthe same pattern of lipid synthesis in response to light intensity.The relative abundance of acetyl CoA carboxylase significantlydecreased in nitrogen limited cultures grown at low dilutionrates (µ<0.72day^–1). A fairly good linear correlationwas measured between the cellular content of ACCase and theenzyme activity in cultures grown under nitrogen limiting conditions.Furthermore, in nitrogen limited cultures, the cellular fattyacid content was linearly related to the cell capacity to producemalonyl CoA, the end product of ACCase and the building blockin fatty acid synthesis. (Received November 20, 1990; Accepted January 17, 1991)     

Decadal change in zooplankton seasonal succession in the Bahia Blanca estuary, Argentina, following introduction of two zooplankton species

Seasonal zooplankton succession (mainly of the mesozooplankton)in the inner zone of Bahía Blanca estuary during theperiod 1990–1991 was compared to that from the period1979–1980 in order to detect changes having taken placein 10 years. Taxonomic composition, zooplankton abundance, speciesoccurrence and temperature–salinity conditions were studiedwithin the two annual cycles. This estuarine ecosystem has beendeeply affected by a population increase and by the rapid growthof industrial activity and maritime traffic over the last twodecades. Several changes in the zooplankton assemblage compositionand structure were detected, probably due to temperature–salinitygradient patterns, which showed discernible differences. Dominance,during winter–spring, of two new invading species, namely,the cirriped Balanus glandula and the copepod Eurytemora americana,causing a decrease in the autochthonous key copepod Acartiatonsa, was one of the principal features of the period 1990–1991.Seasonal changes in diversity and species richness, as wellas differences in the multivariate general pattern of the zooplanktoncommunity structure with a consequent decrease in the communitystability during the second period, were also observed.     

Effects of fire season and soil fertility on clonal growth in a pyrophilic forb,Pityopsis graminifolia (Asteraceae)

We experimentally manipulated fire season in a longleaf pine sandhill community in north Florida in 1990 and 1992. We determined the size and demography of shoots, rhizomes, and clones of Pityopsis graminifolia from late 1990 to early 1993. In addition, we examined shoot responses to seasonal variation in canopy/litter removal and soil fertility in 1992. May fires caused a higher short-term rate of increase in shoot density than did either January fires or August fires. The combination of canopy/litter removal and mineral nutrient addition as part of the clipping experiment revealed a similar effect on shoot density in May. Fire season influenced clone structure. May fires resulted in greater numbers of shoots/clone than did January or August fires. January-burned plots had clones and rhizomes that contained larger (but fewer) shoots than did May-burned or August-burned plots. We suggest that such variation in clone structure may indicate a greater capacity of clones to grow laterally following May fires than following either January or August fires. This capacity is positively associated with the likelihood that longleaf pine savannas will be burned by lightning fires at different times during the year.     

Structure and Characterization of a Gene for Light-Harvesting Chi a/b Binding Protein from Rice

The gene for the light-harvesting chlorophyll a/b binding proteinfrom rice was cloned and se-quenced. The clone contains a 798-bpcoding sequence, which is identical to that of a cDNA for typeI LHCPII (Matsuoka 1990), and its 5'- and 3'-flanking regions.The coding region of this gene is not interrupted by interveningsequences, as reported for type I genes from other plants. Inthe 5'-flanking region, typical TATA and CAAT boxes are located30 and 92 bp upstream from the capping site (positions –30and –92), respectively. A putative phytochrome-responsiveelement (AAGATAAGG) is located at position –65 betweenthe TATA and CAAT boxes. Comparison of sequences in the 5'-flankingregions between this gene and genes for LHCPII from other gramineousplants indicates that the rice sequence has no apparent homologyto that of wheat. However, the rice sequence is highly homologousto the maize sequence, not only around the TATA and CAAT boxesbut also in regions further upstream. To investigate the promoter activity of the 5'-flanking regionof the gene, a chimeric gene was constructed by fusing the 5'-flankingregion to the coding sequence for ß-glucuronidase(GUS), and this chimeric gene was introduced into tobacco. Thehighest activity of GUS was observed in leaf tissue, indicatingthat the 5'-flanking region of the gene can act as a promoterin an organ-specific manner in tobacco. Histochemical analysisin situ was also performed to determine where GUS activity wasexpressed. The highest activity was found in leaf mesophyllcells. High activity was also observed in the vascular systemof stems and petioles, and low activity was found in root tissue. (Received August 20, 1990; Accepted January 21, 1991)     

Finding hydrophobic microdomains using an object-oriented database

A procedure for finding clusters of adjacent residues in proteinhydrophobic cores—hydrophobic microdomains—has beenproposed by Plochocka et al. A program is presented that findshydrophobic microdomains, making use of protein structure datastored in an object-oriented database and the list-processingfeatures of Prolog. Alternative definitions for hydrophobicmicrodomains are explored. Results are presented for haemoglobin. Received on January 15, 1990; accepted on June 28, 1990     

A scale-independent signal processing method for sequence analysis

In this paper, we present methods to detect and localize patternsin biologically related protein sequences (family). The patternscommon to the sequences of the family are detected by usingFourier analysis. No previous scales (codes) are needed, theyare actually produced as a result of the analysis procedure,together with the frequencies of the Fourier decompositions.Characteristic features of the family are thus expressed as(code–frequency) pairs. Various tools are proposed inorder to localize the patterns, to compare the codes, and toevaluate the proximity of an arbitrary sequence to the investigatedfamily. The general strategy is illustrated on a family composedof proteins Received on October 17, 1989; accepted on January 16, 1990     

The Pattern of Abortion of Developing Seeds in Lolium perenne L.

The pattern of seed abortion was followed in each floret offour centrally positioned spikelets in inflorescences of L.perenne from field plots given zero ( –F) or 150 kg Nh^–1 ( + F). There was severe lodging prior to anthesisin the +F plots and control inflorescences were compared withthose held in an erect position and with others reduced to fourcentral spikelets. In the - F plots there was only very limitedlodging and erect control inflorescences were compared withthose reduced to four central spikelets. Observations were madeover a 3-week period and the pattern of seed abortion was verysimilar in all of the treatments. Approximately half of thedeveloping seeds in each spikelet were lost by abortion andthere was a similar degree of loss from all florets. The numberof abortions increased greatly with time and approx. one-thirdwere of ovaries and two-thirds were of seeds at a very earlystage of development (1–2 mm in length and without chlorophyllformation). The effect of nitrogen fertilizer was to increaseboth the number of florets per spikelet and the mean weightper seed. The results are discussed in terms of the availabilityof resources to sustain seed development and growth; it is concludedthat the high degree of abortion may be due to genetic defectsassociated with outbreeding rather than with a shortage of nutritionalfactors     

The Variation in Response to Light Intensity and Carbon Dioxide Concentration Shown by Two Cultivars of Chrysanthemum morifolium Grown in Controlled Environments at Two Times of Year

The growth of the cultivar Golden Princess Anne (G.P.A.) wasstudied in controlled announcement cabinets in a range of lightconditions (125–375 J cm^–2 8-h day^–1) andcarbon dioxide concentrations (325–1500 ppm) in all combinationsPlants obtained in January and grown from January to April showedgreater final total dry weight and flower dry weight at bothhigher light intensity and higher carbon dioxide concentrationwith a strong positive interaction between them, whereas plantsobtained in September and grown from September to December didnot respond much to increased carbon dioxide concentration andthere was only a small positive interaction with light intensity.The plants grown from January to April had larger final leafareas, larger mean leaf-area ratios due mainly to larger specificleaf areas, and higher mean specific leaf-water contents comparedwith September–December plants. Despite the differencein specific leaf-water content, leaf area was almost the samelinear function of absolute leaf-water content at both timesof year. The other vegetative parts also had higher specificwater contents throughout the January–April experimentand the lateral branches were longer when compared with thecorresponding values for September–December Flower developmentwas slightly faster in September–December and the plantsbore on average one flowering branch less compared with January–Aprilplants. Plants in the lower light and carbon dioxide conditions hadlower unit leaf rates, but for plants of similar total dry weightthe effects of this on dry-matter increment were partially offsetby larger leaf areas at both times of year. The January–Aprilplants had greater leaf areas than September–Decemberplants of similar unit leaf rate and total dry weight. The cultivar Bright Golden Anne (B.G.A ) showed effects whichwere in the same direction but smaller in magnitude, tendingto diminish the differences between the times of year For example,the positive interaction in total plant dry weight was smallerin January–April compared with G P A , but larger in September–December.Leaf area, leaf-area ratio, specific leaf area, specific watercontent of leaf, stem, and root, and lateral branch length,were all larger for B G A in corresponding treatment-combinationsin two January–April experiments than in a September–Decemberone, although the difference between the times of year was smallerthan for G.P.A except for leaf area which was relatively butnot absolutely smaller Dry-matter increment and leaf area showedan inverse relationship for plants of the same total dry weight,as in G P A. In January–April B G.A plants of similarunit leaf rate and total dry weight also had greater leaf areasthan in September–December but the differences were notso large as for G.P.A Total dry-matter production was slightlygreater for B.G.A. in January–April and considerably greaterin September–December compared with G P A , and at bothtimes of year B.G.A. was more leafy, with higher specific watercontents for the vegetative parts. It was not possible to determine the cause of the differencesin growth obtained at the two times of year. It could have arisenbefore the cuttings were removed from the stock plants, duringpropagation, or during the course of the experiments in thegrowth cabinets.     

Soil and vegetation response to thinning White Cypress Pine (Callitris glaucophylla) on the North Western Slopes of New South Wales, Australia

Dense White Cypress Pine (Callitris glaucophylla J. Thompson and L.A.S. Johnson) regrowth occurs frequently across previously cleared landscapes in New South Wales (NSW), and is thought to adversely affect agricultural production and to cause land degradation. The NSW Native Vegetation Act (2003) requires that management of native vegetation including pre-1990 regrowth must ‘improve or maintain’ site condition, yet there is currently limited information regarding techniques for the optimum management of C. glaucophylla in this regard. We conducted a preliminary study to examine floristic composition, soil condition (to 50 cm) and carbon storage under ‘Dense’ (dense regrowth), ‘Thinned’ (dense regrowth thinned 2000/2001) and ‘Un-colonised’ (pasture not yet recolonised by C.␣glaucophylla) plots on private lands in NSW. Reduced tree density from thinning resulted in increased biomass of the remaining individual trees. Un-colonised plots had significantly more groundcover than thinned plots, which had significantly more groundcover than dense plots. Differences in plant diversity however, were explained by site factors rather than land use. Soils in the dense plots were the most acid but soil pH was significantly higher in thinned plots and pH was highest in soil of the un-colonised plots. Mean values for carbon, nitrogen, sulphur and extractable phosphorus varied among sites, although each were significantly more abundant in the mineral soil of dense and thinned plots compared with un-colonised plots, suggesting that thinning had had a minimal effect on the soil parameters assessed. Accounting for all site components, site carbon storage was significantly higher in dense and thinned plots compared with un-colonised plots due to elevated levels of soil and litter carbon as well as the presence of trees. The results indicate that thinning dense C. glaucophylla can maintain and (by some measures) improve site condition. However, given the variability in some of the parameters assessed, further study across a wider range of soil types and rainfall gradients is proposed.     

Population structure and swarm formation of the cyclopoid copepod Dioithona oculata near mangrove cays

The cyclopoid copepod Dioithona oculata forms swarms in water>30 on deep among prop roots of red mangroves (Rhizophoramangle) which fringe protected areas of two lagoonal cays, TwinCays, Belize. During 7 of 8 months surveyed by in situ observation,swarms were present but differed in size from small cylindricalswarms (5–10 cm diameter) to bands extending up to 1200m Swarms were never observed at night Swarms formed at dawnwhen light intensities reached an average value of 13.82 (logioquanta cm^–Abstract. s^–1) and dispersed at dusk atsimilar intensities Swarms observed in June formed earlier anddispersed later in the day than swarms observed in January,their swarming behavior followed seasonal changes in light intensityMean dioithonan density in swarms (10 ml^–1) was much higherthan the mean density (0 15 ml^–1) of non-swarming dioithonansaround mangrove prop roots. In open water 3–5 m away fromthe mangroves, mean dioithonan density was 7 9 x 10^–5ml¹ during the day, and 2 68 x10^–3 ml^–1 at nightSwarms were composed predominantly of adults and copepodid stagesIV and V, although younger copepodid stages could be presentNauplii were never present. The ‘average copepodid stage’for all 95 swarms sampled was 5 3, where 6 0 represents a swarmwith only adults In open water 3–5 m away from the mangroves,the youngest copepodids (stage one) dominated the dioithonanpopulation during the day. At night when swarms dispersed toopen waters, average copepodid stage was higher (3 5) comparedwith the day value (1.2) in open waters. Although densitiesin swarms were higher in June than January, average copepodidstage in June was higher (5 6) than that in January (4.9). Ahigher percentage of adults were females during June than January.Therefore higher densities did not result from increases ofsmaller stages in swarms, but perhaps changes in behavior orpopulation structure.     

Emissions of nitrous oxide from three tropical forests in Southern China in response to simulated nitrogen deposition

Emissions of nitrous oxide (N₂O) from the soil following simulated nitrogen (N) deposition in a disturbed (pine), a rehabilitated (pine and broadleaf mixed) and a mature (monsoon evergreen broadleaf) tropical forest in southern China were studied. The following hypotheses were tested: (1) addition of N will increase soil N₂O emission in tropical forests; and (2) any observed increase will be more pronounced in the mature forest than in the disturbed or rehabilitated forest due to the relatively high initial soil N concentration in the mature forest. The experiment was designed with four N treatment levels (three replicates; 0, 50, 100, 150 kg N ha⁻¹ year⁻¹ for C (Control), LN (Low-N), MN (Medium-N), and HN (High-N) treatment, respectively) in the mature forest, but only three levels in the disturbed and rehabilitated forests (C, LN and MN). Between October 2005 to September 2006, soil N₂O flux was measured using static chamber and gas chromatography methodology. Nitrogen had been applied previously to the plots since July 2003 and continued during soil N₂O flux measurement period. The annual mean rates of soil N₂O emission in the C plots were 24.1 ± 1.5, 26.2 ± 1.4, and 29.3 ± 1.6 μg N₂O–N m⁻² h⁻¹ in the disturbed, rehabilitated and mature forest, respectively. There was a significant increase in soil N₂O emission following N additions in the mature forest (38%, 41%, and 58% when compared to the C plots for the LN, MN, and HN plots, respectively). In the disturbed forest a significant increase (35%) was observed in the MN plots, but not in the LN plots. The rehabilitated forest showed no significant response to N additions. Increases in soil N₂O emission occurred primarily in the cool-dry season (November, December and January). Our results suggest that the response of soil N₂O emission to N deposition in tropical forests in southern China may vary depending on the soil N status and land-use history of the forest.