FASTPAT: a fast and efficient algorithm for string searching in DNA sequences

A new string searching algorithm is presented aimed at searchingfor the occurrence of character patterns in longer charactertexts. The algorithm, specifically designed for nucleic acidsequence data, is essentially derived from the Boyer –Moore method (Comm. ACM, 20, 762 – 772, 1977). Both patternand text data are compressed so that the natural 4-letter alphabetof nucleic acid sequences is considerably enlarged. The stringsearch starts from the last character of the pattern and proceedsin large jumps through the text to be searched. The data compressionand searching algorithm allows one to avoid searching for patternsnot present in the text as well as to inspect, for each pattern,all text characters until the exact match with the text is found.These considerations are supported by empirical evidence andcomparisons with other methods.     

Possible Active Site of the Sweet-tasting Protein Thaumatin

Epitopes on thaumatin and monellin were studied using the PEPSCAN-technology.The antibodies used were raised against thaumatin. Only antibodiesthat, in an ELISA, both recognized thaumatin and monellin wereused in the PEPSCAN-analyses. On thaumatin two major overlappingepitopes were identified. On monellin no epitopes could be identified.The identified epitope region on thaumatin shares structuralfeatures with various peptide and protein sweeteners. It containsan aspartame-like site which is formed by Asp21 and Phe80, tipsof the two extruding loops KGDAALDAGGR_19–29 and CKRFGRPP_77–84,which are spatially positioned next to each other. Furthermore,sub-sequences of the KGDAALDAGGR^19–29 loop are similarto peptide-sweeteners such as L-Asp-D-Ala- L-Ala-methyl esterand L-Asp-D-Ala-Gly-methyl ester. Since the aspartame-like Asp21-Phe80site and the peptide-sweetener-like sequences are also not presentin non-sweet thaumatin-like proteins it is postulated that theKGDAALDAGGR_19–29 and CKRFGRPP_77–84 loop containimportant sweet-taste determinants. This region has previouslynot been implicated as a sweet-taste determinant of thaumatin.Chem. Senses 20: 535–543, 1995.     

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     

Deamination features of 5-hydroxymethylcytosine,a radical and enzymatic DNA oxidation product

Geometric consequences of electron delocalization were studied for all possible adenine tautomers in aqueous solution by means of ab initio methods {PCM(water)//DFT(B3LYP)/6-311+G(d,p)} and compared to those in the gas phase {DFT(B3LYP)/6-311+G(d,p)}. To measure the consequences of any type of resonance conjugation (π-π, n-π, and σ-π), the geometry-based harmonic oscillator model of electron delocalization (HOMED) index, recently extended to the isolated (DFT) and hydrated (PCM//DFT) molecules, was applied to the molecular fragments (imidazole, pyrimidine, 4-aminopyrimidine, and purine) and also to the whole tautomeric system. For individual tautomers, the resonance conjugations and consequently the bond lengths strongly depend on the position of the labile protons. The HOMED indices are larger for tautomers (or their fragments) possessing the labile proton(s) at the N rather than C atom. Solvent interactions with adenine tautomers slightly increase the resonance conjugations. Consequently, they slightly shorten the single bonds and lengthen the double bonds. When going from the gas phase to water solution, the HOMED indices increase (by less than 0.15 units). There is a good relation between the HOMED indices estimated in water solution and those in the gas phase for the neutral and ionized forms of adenine. Subtle effects, being a consequence of intramolecular interactions between the neighboring groups, are so strongly reduced by solvent that the relation between the HOMED indices and the relative energies for the neutral adenine tautomers seems to be better in water solution than in the gas phase.

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.     

Transforming a set of biological flat file librariesto a fast access network

SRS (Sequence Retrieval System), an indexing system for flatfile libraries, provides fast access to individual library entriesvia retrie by keywords from rious data fields. SRS is now alsoable to build indices using cross–references that mostlibraries provide. Fifteen libraries of DNA and protein sequencesand structures have been selected. These libraries interactwith at least one other by means of cross–references.Indexing these cross–references allows a complete networkof libraries to be built. In the network an entry from one librarycan be linked in principle to every other library. If two librariesare not directly cross–referenced, the linkage can bemade with a succession of single links between neighbouring,cross–referenced libraries. A new operator has been addedto the query language of SRS for convenient specification oflinks amongst complete libraries or entry sets generated byprevious queries on particular libraries. All the informationin the network can now be used to retrieve an entry in a specificlibrary, e.g. the full information given in amino acid sequenceentries from SwissProt can now be used to retrieve related tertiarystructure entries from PDB. Furthermore, a search in a singlelibrary can be extended to a search in the complete librarynetwork, e.g. all entries in all databases pertaining to elastasecan be found.     

The time course of solitary nucleus gustatory responses: influence of stimulus and site of application

The responses of 64 neurons in the nucleus of the solitary tract(NST) of the rat were recorded while independently stimulatingthe anterior tongue (AT) and the nasoincisor ducts (NID) withsucrose and NaCl. The time course of this activity has beenanalyzed by averaging the responses (500 ms bins) to each stimulus:receptorsubpopulation combination across neurons. Regardless of thesite of stimulus application, the average time course of theNaCl responses was similar: both peaked rapidly (1.0–1.5s), with a peak/tonic ratio of >2:1. On the other hand, whenthe AT or NID was stimulated with sucrose, the average timecourse of the responses varied. The mean sucrose:NID responserose rapidly (1.0–1.5 s) to its maximum, which was 2.Oxthe magnitude of the tonic response. Sucrose on the anteriortongue elicited a response with a time course that differedfrom all other responses studied: it peaked slowly (3.5–4.0s), and exhibited a peak/tonic ratio of only 1.5:1. In distinctionto what had been observed for peripheral fibers, a finer-grainedanalysis of individual NST responses evoked by stimulating theAT and NID with sucrose revealed minimal evidence for regularbursting.     

Modification of CD43 and other lymphocyte O-glycoproteins by core 2 N-acetylglucosaminyltransferase

CD43, the major leukocyte sialoglycoprotein, is expressed onT lymphocytes in two predominant glycoforms. CD43 115 kDa isa pan T cell marker and is specifically recognized by the monoclonalantibody S7. CD43 130 kDa is associated with T cell activationand is specifically recognized by the monoclonal antibody 1B11.The thymoma EL-4 has been identified to express mainly CD43115 kDa and little or no CD43 130 kDa. Transfection of EL-4cells with core 2 ß16N-acetylgIucosaminyltransferase(C2GnT), an enzyme in the O-glycan biosynthesis pathway, resultedin an enhanced expression of the 1B11 epitope, CD43 130 kDa,and a loss of expression of the S7 epitope, CD43 115 kDa. Analysisof CD43 by SDS-PAGE revealed that CD43 in C2GnT transfectedEL-4 cells has a molecular weight of 125 kDa compared to 115kDa in nontransfected or control transfected EL-4 cells. SDS-PAGEanalysis of three other lymphocyte O-glycoproteins, CD44, CD45,and RPTPa., revealed that C2GnT expression resulted in a molecularweight increase of approximately 3–5 kDa for each of thesethree cell surface glycoproteins. Our data indicate that, whileCD43 may be a predominant substrate for C2GnT, other lymphocyteO-glycoproteins are also modified by this glycosyltransferase.Increased reactivity of cells with the monoclonal antibody 1B11,which specifically detects the expression of murine CD43 130kDa, may thus be a marker of increases in branching of O-linkedglycans generally. CD43 core 2 N-acetylglucosaminyltransferase lymphocyte glycoproteins     

The Diffusion of KCI from Micro-electrodes

The diffusion of salt from the tips of 3 M KCI filled micro-electrodesis measured. The leakage of KCI in 3 min is found to be 5.70x 10^–12–1.08 x 10^–11 mol for tips of 0.2–0.6µm diameter, and 2.70 x 10^–11 mol for tips of 0.6–1.0µm diameter. The observed leakages compare with estimatesbased on the diffusion coefficient of KCI and micro-electrodegeometry. The results confirm that the use of 3 M KCI in micro-electrodesmay lead to serious contamination of impaled cells providedthe electrode tips remain unoccluded.     

Biosynthesis of poly(ɛ- l-lysine)s in two newly isolated strains of Streptomyces sp.

The biosynthesis of poly(ɛ-l-lysine) (ɛ-PL) in the two newly isolated strains of Streptomyces lydicus USE-11 (USE-11) and Streptomyces sp. USE-51 (USE-51) was studied by a newly developed two-stage culture method of cell growth at pH 6.8 and ɛ-PL production at pH 4.5. USE-11 synthesized ɛ-PL consisting of about 28 residues at a high production level, whereas USE-51 did the polymer with 15 ones at a low level. The secreted ɛ-PLs in culture media were digested in a neutral pH range with a peptide hydrolase(s) produced by the ɛ-PL producers. The optimum production levels were presumed to be dependent upon the inherent ɛ-PL synthesis machinery of each producer. The production in USE-51 was sharply dependent upon cell density as was often observed in the production of antibiotics, whereas that in USE-11 was scarcely affected by the density. The was found to be essential for the ɛ-PL production in both strains. This might suggest the involvement of a thiol group in the polymerization reactions including the activation of l-lysine. This study indicates that USE-11 is a most suitable strain for the exploration of the ɛ-PL biosynthesis at the molecular level as well as for the technical applications.Electronic supplementary material Electronic supplementary material is available if you access this article at and is accesible for authorized users.An erratum to this article can be found at     

Effective Thickness and Resistance of the Air Boundary Layer Adjacent to Spherical Plant Parts

Using existing heat transfer data a rather simple expressionis developed for the effective thickness of the boundary layerof air adjacent to spheres. The calculated boundary layer thicknessagreed fairly well with that determined for water vapour diffusionfrom a wet spherical surface 5.90 cm in diameter for wind velocitiesfrom 10 to 1000 cm s^–1. At a turbulence intensity representativeof field conditions (0.5), the measured boundary layer thicknessaveraged 11 per cent less than for a relatively low turbulenceintensity of 0.01. For wind velocities up to 100 cm s^–1,the resistance of the boundary layer for water vapour diffusionwas actually greater than the resistance of the basidiocarpsof Lycoperdon perlatum, L. polymorphum, and Scleroderma australe.The tissue resistance for water vapour movement from the fruitingbodies of other members of the Basidiomycetes was also low (below10 s cm^–1), while the resistance of 20 different sphericalfruits ranged from 30 to over 5000 s cm^–1. The thicknessof the air boundary layer for spheres can depend on the squareroot of a characteristic dimension divided by the wind velocity,as has already been shown for cylindrical and flat plant material.     

An automated computer vision and roboticsbased technique for 3-D flexible biomolecular docking and matching

The generation of binding modes between two molecules, alsoknown as molecular docking, is a key problem in rational drugdesign and biomolecular recognition. Docking a ligand, e.g.,a drug molecule or a protein molecule, to a protein receptor,involves recognition of molecular surfaces as molecules interactat their surface. Recent studies report that the activity ofmany molecules induces conformational transitions by ‘hinge-bending’,which involves movements of relatively rigid parts with respectto each other. In ligand–receptor binding, relative rotationalmovements of molecu–lar substructures about their commonhinges have been observed. For automatically predicting flexiblemolecular interactions, we adapt a new technique developed inComputer Vision and Robotics for the efficient recognition ofpartially occluded articulated objects. These type of objectsconsist of rigid parts which are connected by rotary joints(hinges). Our approach is based on an extension and generalizationof the Geometric Hashing and Generalized Hough Transform paradigmfor rigid object recognition. Unlike other techniques whichmatch each part individually, our approach exploits forcefullyand efficiently enough the fact that the different rigid partsdo belong to the same flexible molecule. We show experimentalresults obtained by an implementation of the algorithm for rigidand flexible docking. While the ‘correct’, crystal–boundcomplex is obtained with a small RMSD, additional, predictive‘high scoring’ binding modes are generated as well.The diverse applications and implications of this general, powerfultool are discussed     

The Production of the Striga and Orobanche Germination Stimulants by Maize Roots: II. CONDITIONS OF SYNTHESIS IN THE ROOT

Six serial segments, each 3·0 mm. in length, have beenexcised from the tip backwards along the maize root and groupsof each fragment have been aerated in water and in solutionsof sugars for varying times. The amounts of the complex of Orobancheand Striga germination stimulants which accumulate in the culturefluids have been assessed and compared with the amounts initiallypresent in the tissue at the time of excision from the root. It is shown that with each fragment more of the complex appearsexternally when sugar is supplied. 10^–2 M. solutions ofglucose, fructose, or sucrose promote an optimal effect. Theamounts in the external solutions are inversely proportionalto the initial contents of the segments. The first segment (0–3mm.) contains the highest proportion of the complex initially,but when immersed in water or the sugar solution very littleof it appears externally. The second segment (3–6 mm.)contains the least initial quantity of the complex but in wateror sugar produces considerably more than any other segment andmore than is originally present. As the series is traversedfrom segments 2 to 6, the segments have progressively largerinitial contents than has segment 2, but after aeration in thesugar solutions the amounts accumulating externally are lessthan with segment 2 and decrease with their increasing distancefrom the root tip. The significance of these observations is discussed.     

Discrimination of female sex pheromone by male Trichoplusia ni (Hubner)

The olfactory discrimination process of male cabbage loopermoths, Trichoplusa ni (Hübner), was assessed by measuringtheir response to one of two emission sources within a windtunnel. The males discriminated between (1) Z7–12:Ac concentrations;(2) Z7–12:Ac alone and the volatile emission from excisedfemale sex pheromone glands; and (3) Z7–12:Ac and theemission from a mixture of six synthetic pheromone componentsthat mimics the volatile emissions of a female gland. Althoughmales could discriminate between a freshly excised female sexpheromone gland and 7.4x 10^–11 M Z7–12:Ac, theycould not discriminate between a gland and 78.5x10^–11M Z7–12:Ac. Males also could not discriminate betweenthe mixture of six volatile compounds and 28.7x10^–11 Mof Z7–12:Ac. The data show that male cabbage looper mothshave difficulty discriminating between Z7–12:Ac aloneand in mixtures with other female-emitted volatile compounds.     

Mesozooplankton grazing under conditions of extreme eutrophication in Guanabara Bay, Brazil

The objective of the present study was to quantify mesozooplanktongrazing in the eutrophic waters of Guanabara Bay. Mesozooplankton(>200 µm) was dominated by the copepods Acartia lilljeborgi,Acartia tonsa, Parvocalanus crassirostris and Paracalanus furcatus.Dinoflagellates, specifically the species Prorocentrum triestinum,were an important group for mesozooplankton nutrition, beingingested in significant amounts during all experiments. On average,12.3 ± 2.9 P. triestinum cells were ingested copepod^–1min^–1 (other dinoflagellates: 11 ± 8 cells copepod^–1min^–1). Filamentous cyanophyceae and nanoplankton wereingested in one experiment each, but the mesozooplankton communitygenerally preferred dinoflagellates to these groups, which werealways abundant in the water column. Euglenophyceae were notingested, although they dominated in one experiment. Mesozooplanktoningested, on average, only 0.2% of the nano- and microplanktonbiomass per day. The results suggest that grazing was not acontrolling process for the nano- and microplankton communityin the study area. Addition of zoeae larvae of Chasmagnatusgranulata (Decapoda: Brachyura: Grapsidae) in one experimenthad a significant effect on the mortality of adult copepods,probably due to a predator–prey relationship.     

Growth and Photosynthesis in Sorghum bicolor Infected with Striga hermonthica

Sorghum plants were grown in the laboratory with the root systemof each plant split between two pots. Three split pot treatmentswere established: (– –) treatment, where both halvesof the root were free from Striga; (– +) treatment, wherethe soil in one half of the pot had been inoculated with Strigaseed; (+ +) treatment, where the soil in both halves of thepot had been inoculated with Striga. Seed, stem and leaf weight were reduced by 82, 60 and 26 percent respectively in (+ +) plants compared to (– –)plants. Partially infected plants (– +) behaved similarlyto (+ +) plants. Rates of light saturating carbon dioxide fixation in (+ +) and(– +) plants were only 60 per cent of those measured in(– –) plants. This reduction was independent ofchanges in stomatal conductance. The effects of Striga on the growth and photosynthesis of sorghumappear to be independent of the degree of parasitism to whichthe host is subjected. The difference in production betweeninfected and uninfected plants was greater than could be accountedfor in term of competition with the parasite for resources,and Striga appears to have a pathological effect on the host. Sorghum, Striga, parasitic angiosperm, growth, photosynthesis     

Water and Seed Survival

Between about –350 and –14 MPa the rate of lossof viability in orthodox seeds is a positive function of waterpotential. The relative effect of water potential has been analysedin an oily seed (lettuce) and a non-oily seed (barley) and foundto be more or less identical. The lower limit for the relationin various species coincides with a seed moisture content (wetbasis) between about 2 and 6%. Below this level there is littleor no improvement in longevity with reduction in moisture content.The upper limit coincides with moisture contents of between15 and 28%, depending on whether the seeds are oily or non-oily.A water potential of about –14 MPa is the threshold forrespiration which increases more-or-less linearly with increasein water potential above this level. Above this threshold, andproviding oxygen is available to sustain respiration, seed longevityincreases with increase in water potential except that, unlessthe seeds are dormant, germination may be initiated at a waterpotential of about –1·5 to –0·5 MPa.In the absence of oxygen there may be a slight further declinein longevity with increase in water potential above –14MPa before longevity reaches a minimum value Since they cannot be dried very much without immediate lossof viability, recalcitrant seeds survive longest in the presenceof oxygen at maximum water potential commensurate with preventinggermination. The threshold water potential for immediate lossof viability has not been determined for most species but itis probable that it is close to the water potential typicalof the permanent wilting point in these plants, say –2MPa Lactuca saliva L., lettuce, Hordeum oulgare L., barley, seed storage, moisture content, relative humidity, water potential, temperature, oxygen     

A Method for in Vitro Storage of Lolium multiflorum Lam

A means of storing Lolium multiflorum Lam. stock plants in vitrohas been developed over a period of three years. Variousexplantsand cultureconditions were examined. Shoot tips 0.3–0.9mm long were found to be best for establishing storage culturesbecause they gave a high yield of plantlets in culture and importantpathogens are eliminated. For sub-culturing, after each annualcycle of storage at 2–4 °C, shoot tips, tiller buds,tiller bases and nodes can be used. Tiller buds were most abundantand best for increasing the number of stored plantlets whennecessary. There was no advantage of including an auxin in theculture medium for shoot tips and Murashige and Skoog's mediumwith 0.2 mg l^–1 kinetin has been adopted for initiating,sub-culturing and storing cultures. The optimum temperaturerange for regenerating plantlets was 20–25 °C. Lightwas necessary for a high rate of plantlet regeneration and lightquality and intensity affected their growth. Lolium multiflorum Lam., ryegrass, storage in vitro, tissue culture     

Tree Suppression and the Self-thinning Rule in a Monoculture of Pinus radiata D. Don

An experiment comparing different initial planting densitiesof Pinus radiata D. Don was established in 1940 at Mt. Burrin south-east South Australia. It had been measured periodicallyto age 40 years. It is shown that after some years the treesof each individual plot of the experiment segregated into agroup of ‘suppressed’ trees which grew little indiameter and a group of actively growing ‘dominant’trees. This is consistent with other work that has suggestedthat monocultures tend to produce a two-tiered canopy. The slopeof the relationship between the logarithm of the mean weightper tree and the logarithm of the density of the various plotsof the experiment (the ‘competition-density effect’)was computed at each age at which the experiment was measured,both for all live trees of the plots and for the dominants only.For this analysis tree weights were estimated using the allometricrelationship between weight and diameter at breast height. Forthe dominants, the slope rapidly declined with age until itapproached – 1.5, which is the limiting slope of the competition-densityeffect or the so-called ‘self-thinning rule’. Whenall live trees of the plots were used, the slope declined slowlywith age but remained far from – 1.5. Previously, theself-thinning rule has been seen as determining the way in whichmortality, i.e. self-thinning, occurs in stands. In the presentwork, the rule is found to apply to the larger, actively growingtrees of the stands soon after they start to suppress the smallertrees and long before substantial mortality has occurred inmany stands. Thus tree suppression, rather than mortality, isseen to determine the rule. The pattern of diameter growth oftrees of the various stands of the experiment is found to beconsistent with previous findings that skewness of the frequencydistribution of diameters of trees of stands increases withtime. Pinus radiata D. Don, radiata pine, self-thinning, competition     

A quantitative analysis of the annual phytoplankton cycle of the Magdalena lagoon complex (Mexico)

An annual cycle of the micro- and nanophytoplankton cell densitiesof whole water samples in combination with the species composition,distribution and diversity of the microphytoplankton fractionin the Magdalena lagoon system, Mexico, has been studied ona bi-monthly basis. Two major patterns were detected: from Novemberto May, high microphytoplankton densities (0.5–1.5 10⁶cells l^–1 prevail throughout a large part of the investigatedarea; from late spring to late autumn cell densities are muchlower (5–250 10³ cells l^–1). During each perioda number of microplankton assemblages occur, each with its characteristicdiversity and stability. The distribution and density of themicrophytoplankton is clearly related to the presence of nutrient-richwater pockets and the prevailing winds for part of the year,as documented in earlier hydrological studies. The nanophytoplanktonplayed a minor role during most of the year; this fraction dominatedquantitatively in only a few cases. Based on these data, theMagdalena lagoon complex can be considered a very productivearea. This is further substantiated by the presence of largequantities of several sardine and mackerel species, feedingalmost exclusively on microphytoplankton. This reveals the existenceof an important short chain pathway in the food web of thiscoastal lagoon system