An Improved Cosmid Vector for the Nested Deletion Method Using the Bacteriophage T3 DNA Packaging System

We constructed a new cosmid vector suitable for the previouslydeveloped nested deletion method which used the in vitro DNApackaging system of bacteriophage T3. The first step of thismethod is linearization of a cosmid clone to be packaged, andwe previously introduced cleavage at the cos site using -Terminase,but optimization of the reaction conditions was required forcomplete digestion because of its instability. In the newlyconstructed vector, pAT5, the sites of 4 different restrictionenzymes, Sse8387I, Asc I, Fse I and Pme I, each of which recognizesan 8-bp sequence (8-base cutter) were introduced in the vicinityof the cos site. In addition, the species of restriction sitesfor cloning were increased to broaden its application. The cosmidclone constructed by this new vector could be linearized atone of the 8-base cutter sites which are assumed to rarely occurin the genome, and followed by in vitro packaging, nested deletionclones were successfully prepared.     

Application of N-terminally Truncated DNA Polymerase from Thermus thermophilus ({Delta}Tth Polymerase) to DNA Sequencing and Polymerase Chain Reactions: Comparative Study of {Delta}Tth and Wild-Type Tth Polymerases

N-Terminally truncated DNA polymerase from Thermus thermophilus(Tth polymerase) lacking 5'-3' exonuclease activity was usedfor DNA sequencing and polymerase chain reaction (PCR). In contrastto the high background of the sequencing ladder observed withthe wild-type Tth polymerase, Tth polymerase gave readable sequencingpatterns which extend up to more than 500 bases from the primersite on cycle sequencing and automated sequencing. The Tth polymerasewas used for the standard and mutagenic PCR, and net amplificationof the DNA and the mutations accumulated during PCR were analyzed.Under mutagenic PCR, the mutation rates were 7.0 x 10^–4(Tth) and 8.3 x 10^–4 (Tth) per nucleotide per cycle ofamplification, which were 4–9 times higher than the ratesunder standard PCR.     

srb: a Bacillus subtilis Gene Encoding a Homologue of the {alpha}-Subunit of the Mammalian Signal Recognition Particle Receptor

We cloned a Bacillus subtilis gene (srb) encoding a homologueof the mammalian signal recognition particle receptor -subunit(SR). The gene is 987 bp in length and encodes a 329-amino acidprotein. The deduced amino acid sequence of the protein shared26.6, 36.2 and 49.7% identity with those of mammalian SR, archaebacterialDP and Escherichia coli FtsY, respectively. The protein containsthree conserved GTP-binding elements like the other three SRPreceptor proteins, though the N-terminal portion of the putativeB. subtilis protein was shorter than the others. Secondary structureprediction showed that an amphipathic -helix is positioned inthe N-terminal region. A defect in srb inhibited cell growthand protein translocation.     

Transmembrane-Domain Trapping: A Novel Method for Isolation of cDNAs Encoding Putative Membrane Proteins

We have developed a method that enables us to isolate cDNAsof putative membrane proteins. The system is designed to isolatea cDNA which can provide the transmembrane domain to the extracellularpart of the IL-2 receptor chain. We constructed a p18Mac vectorby putting part of the IL-2 receptor chain cDNA that encodedits signal sequence and extracellular domain, a cDNA cloningsite and a poly(A) additional signal after a strong promoterSR. If a cloned cDNA provides a transmembrane domain in-frame,the extracellular domain of the IL-2 receptor chain will beexpressed on the surface of the transfected cells. Otherwise,the chimeric protein will be either secreted or retained insidethe transfected cells. We made a cDNA library using p18Mac andscreened for cDNA clones which allowed the expression of theextracellular domain of the IL-2 receptor chain on the cellsurface. Of the 2000 clones screened, 5 clones were scored aspositive. Partial sequence analysis revealed that one cloneencoded the amyloid precursor protein, two others encoded mitochondrialproteins and the rest were new. These results suggest the systemis effective in isolating cDNAs encoding putative membrane proteins.     

DNA Sequencing Directly from a Mixture Using Terminal-Base-Selective Primers

DNA cloning is often used to select and amplify one DNA speciesfrom a mixture. However, the cloning process is complex andlabor-intensive. We have developed a new two-step method forDNA sequencing directly from a mixture. The first is the introductionof a known oligonucleotide (common part) into the terminus ofunknown DNA by ligation. The second is selective DNA sequencingusing primers with two additional nucleotides at the 3' terminusin addition to the common part (terminal-base-selective primers).The primers work only for templates on which the primers perfectlyhybridized. This method was found to be effective for the HindIIIdigestion products of phage.     

Integrated likelihood functions for non-Bayesian inference

Consider a model with parameter = (, ), where is the parameterof interest, and let L(, ) denote the likelihood function. Oneapproach to likelihood inference for is to use an integratedlikelihood function, in which is eliminated from L(, ) by integratingwith respect to a density function (|). The goal of this paperis to consider the problem of selecting (|) so that the resultingintegrated likelihood function is useful for non-Bayesian likelihoodinference. The desirable properties of an integrated likelihoodfunction are analyzed and these suggest that (|) should be chosenby finding a nuisance parameter that is unrelated to and thentaking the prior density for to be independent of . Such anunrelated parameter is constructed and the resulting integratedlikelihood is shown to be closely related to the modified profilelikelihood.     

Assignment of 82 Known Genes and Gene Clusters on the Genome of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC6803

We have previously constructed the physical map of a cyanobacterium,Synechoystis sp. strain PCC6803 on the basis of restrictionand linking clone analysis. Since a total of 82 genes and geneclusters have been isolated from this strain, most of whichare involved in oxygenic photosynthesis, portions of their sequenceswere amplified by the PCR method and assigned on the physicalmap of the genome by hybridization with restriction fragments,ordered clones, which were obtained from cosmid and libraries,and long PCR-products. An exception was the gene psbG2 whichwas mapped on an extra-chromosomal unit of 45 kb. Since geneticmaps of some of genes assigned above, especially those for photosynthesis,have been reported for two other cyanobacterial strains, Anabaenasp. PCC7120 and Synechococcus sp. PCC7002, gene organizationswere compared among the three strains. However, no significantcorrelation was observed, suggesting that rearrangement of genesoccurred in the respective strains during or after establishmentof the species.     

Organization of the Chicken Histone Genes in a Major Gene Cluster and Generation of an Almost Complete Set of the Core Histone Protein Sequences

We present a detailed picture of the disposition of the histonegenes in the chicken genome and an almost complete set of thecore histone protein sequences. Thirty-nine histone genes, sixH1, nine H2A, eight H2B, eight H3 and eight H4, were locatedwithin a histone gene cluster of 110 kb, which was covered byfive cosmid clones and two clones. Results of our sequenceanalyses, together with those reported previously, generateda set of the core histone amino acid sequences as follows: threeH2A variants, four H2B variants,two H3 variants and an H4 protein.     

Multi-Gene Family of Major Surface Glycoproteins of Pneumocystis carinii: Full-Size cDNA Cloning and Expression

The major surface glycoprotein (MSG) of Pneumocystis cariniiplays a crucial role in the fatal pneumonia caused by this organismin AIDS patients. A cDNA encoding a full-length MSG polypeptidewas isolated from a phage library of rat-derived P. cariniicDNAs. The deduced MSG, referred to as the MSG5 subtype, isa 120,765-Da protein composed of 1,076 amino acids and containsan anchoring hydrophobic sequence at the C-terminus of the protein.Sequence analyses of cloned MSG-cDNAs revealed an MSG-gene familywith 70% protein sequence identity between subtypes. P. cariniikaryotype hybridization analyses indicated that the MSG genefamily members are scattered throughout most of the P. cariniichromosomes. These recombinant MSG proteins reacted with theantiserum from P. carinii-infected rats, as expected, and antiserumgenerated against P. carinii-infected mice, indicating the existenceof common determinants in MSG polypeptides. The family of MSGproteins is rich in cysteine residues and these cysteine arehighly conserved in all MSG subtypes regardless of species specificity,suggesting the structural and/or functional importance of thesecysteine. The pathobiological significance of the MSG gene familyand its sequence diversity in P. carinii is discussed.     

Occurrence of mycosporine-like amino acids in the red-tide dinoflagellate Alexandrium excavatum: UV-photoprotective compounds?

Water extracts of the red-tide dinoflagellate Alexandrium excavatumgrown at ‘high’ light intensity (200 µE m^–2s^–1) show a broad absorbance maximum in the UV regionof the spectrum (310–360 nm). Using TLC and reverse-phaseHPLC a series of mycosporine-like amino acids have been characterized:mycosporine-glycine (_max = 310 nm), palythine (_max = 320 nm),asterina-330 (_max = 330 nm), shinorine (_max = 334 nm), porphyra-334(_max= 334 nm), palythenic acid (_max = 337 nm) and the isomericmixture of usujirene and palythene (_max = 359 nm). From theobserved spectral changes during transference from ‘low’(20 µE m^–2 s^–1) to ‘high’ (200µE m^–2 s^–1) light intensities and vice versa,the series of compounds are supposed to be biogenically relatedto one another. The presence of these compounds in A.excavatumis discussed in relation to their possible role in the photoprotectionto deleterious UV radiation.     

On filament width in oceanic plankton distributions

A plankton patch deformed by diffusion, straining flow and biologicalgrowth is demonstrated to have a minimum width, /, which ispurely a function of the effective diffusivity, , and the strainrate, .     

Genotypic Differences in Leaf Water Relations between Brassica juncea and B. napus

Various kinds of measurement of tissue water status were madeseveral times during water stress and recovery in Brassica juncea(cv Canadian Black) and B napus (cv Drakkar) Unstressed plantsof the two species had similar leaf water potentials (_w), solute(_s) and turgor potentials (_p) Values of relative water content(RWC) and the slope of the linear relationship between _p andRWC (_p/RWC) were greater in B napus than in B juncea Statistical correlations of pooled data for the watered andstressed treatments differentiated the relationships among RWC,_w and its components in the two species The major statisticaldifference was that _p/RWC was related to RWC in B napus andto _w and _s in B juncea A decline in _p/RWC with decreasing _sin B juncea may be a mechanism for maintaining _p at low soilwater potentials through maintenance of more elastic cell walls. Brassica juncea, Brassica napus, osmotic adjustment, tissue elasticity, water relations     

Sialylation of n-alkyllactosides, galactosides and glucosides by sialyltransferases from rat liver Golgi vesicles

nAlkyl - and -lactosides, galactosides and glucosides with differentalkyl chain lengths (C₂, C₈, C₁₄, and C₂₀) were synthesizedand used as acceptors for sialyltransferases from rat liverGolgi vesicles. The -galactosides, -glucosides, and both - and-lactosides, were sialylated. Keeping the acceptor concentrationconstant, sialylation rates reached a maximum for the n-octyl- and -lactosides, n-Octyl -galactoside and noctyl -glucoside,respectively. noctyl -glucoside, respectivwly. n-Octyl -galactosideand n-octyl -glucoside were not sialylated. The reaction productswere characterized by TLC. With n-octyl lactoside and galactosideas acceptors, two major sialylation products were formed. Thjeycould be separated by preparative TLC, and their structureswere identified as 2–3 and 2–6 sialylated acceptors,respectively, by a combination of periodated oxidation, NaBD₄reduction,permethylation and subsequent analysis by fast atombombardment mass spectrometry (FAB-MS). The structure of thesingle product obtained from n-ictyl -glucoside was determinedto be the 2–6 sialylated glucoside. Competition experimentswith n-octyl lactoside and lactosylceramide and gangliosideGal1-3GalNAc1-4(NeuAc2–3)Gal1–4Glcbeeta1–1Cer(GM1) as acceptors for sialyltransferases suggested that SAT-I[NeuAc2–3Gal1–4Glc1-1Cer (GM3) synthase] was atleast in least in part responsible for the 2–3 sialylationof n-octyl lactoside. alkylgalactosides alkylglucosides alkyllactosides neoglycolipids sialytransferases     

Effects of Priming and Endosperm Integrity on Seed Germination Rates of Tomato Genotypes: II. GERMINATION AT REDUCED WATER POTENTIAL

Seed germination rates (GR =inverse of time to germination)are sensitive to genetic, environmental, and physiological factors.We have compared the GR of tomato (Lycopersicon esculentum Mill.)seeds of cultivar T5 to those of rapidly germinating L. esculentumgenotypes PI 341988 and PI 120256 over a range of water potential(). The influence of seed priming treatments and removal ofthe endosperm/testa cap enclosing the radicle tip on germinationat reduced were also assessed. Germination time-courses atdifferent 's were analysed according to a model that identifieda base, or minimum, allowing germination of a specific percentage(g) of the seed population (_b(g)), and a ‘hydrotime constant’(_H) indicating the rate of progress toward germination per MPa.h.The distribution of _b(g) determined by probit analysis was characterizedby a mean base (_b) and the standard deviation in _b among seeds(_b). The three derived parameters, _b, _b) and _H, were sufficientto predict the time-courses of germination of intact seeds atany . A normalized time-scale for comparing germination responsesto reduced is introduced. The time to germination at any (t_g())can be normalized to be equivalent to that observed in water(t_g(0)) according to the equation t_g(0)=[l–(/_b(g))]t_g().PI 341988 seeds were more tolerant of reduced and had a morerapid GR than T5 seeds due to both a lower _b and a smaller _H.The rapid germination of PI 120256, on the other hand, couldbe attributed entirely to a smaller _H. Seed priming (6 d in–1.2 MPa polyethylene glycol 8000 solution at 20 ?C followedby drying) increased GR at all >_b(g), but did not lower theminimum allowing germination; i.e. priming reduced _H withoutlowering _b. Removing the endosperm/testa cap (cut seeds) markedlyincreased GR and lowered the mean required to inhibit germinationby 0.7 to 0.9 MPa. However, this resulted primarily from downwardadjustment in _b during the incubation of cut seeds at low inthe test solutions. The difference in _b between intact and cutseeds incubated at high was much less (0.l MPa), indicatingthat at the time of radicle protrusion, the endosperm had weakenedto the point where it constituted only a small mechanical barrier.In the intact seed, endosperm weakening and the downward adjustmentin embryo _b ceased at < –0.6 MPa, while the reductionin _H associated with priming proceeded down to at least –1.2MPa. Based on these data and on the pressure required to pushthe embryos from the seeds at various times after imbibition,it appears that the primary effect of priming was to shortenthe time required for final endosperm weakening to occur. However,as priming increased GR even in cut seeds, priming effects onthe embryo may control the rate of endosperm weakening. Key words: tomato, Lycopersicon esculentum Mill., water potential, germination rate, seed priming, genetic variation     

Water-Relations Parameters of the Phloem. Determinations of Volumetric Elastic Modulus and Membrane Conductivity using an Applied Force Method and Shrinkage and Swelling of Tissues in Solutions at Differing Osmotic Pressure

Water-relations parameters were measured on sections of secondaryphloem from red oak (Quercus borealis michx. f.) and white ash(Fraxinus americana var. biltmoreana [Beadle] J. Wright) usinga linear displacement transducer. Changes in tissue thicknessin response to changes in the osmotic pressure of the bathingsolution were used to calculate the volumetric elastic modulusplus osmotic pressure (_v + ) of the tissue, and an applied forcemethod was used to estimate the time constant for water equilibration(T). The hydraulic conductivity of the cell membranes (L_p) wascalculated utilizing _v + and r values. The time-dependent behaviour of the tissue was much more complexthan originally expected. A correction for a time-dependentprocess that we call ‘drift’ was required to obtainnumbers for _v + . Furthermore, _v + was calculated on two assumptionsin order to relate changes in tissue dimensions to sieve elementparameters. In the first case, a lower limit for _v + of thesieve elements was determined by attributing all changes intissue dimensions to these cells. For red oak the average _v+ on this assumption is 72 bars. Assuming that all cell typeswere equally responsible for the changes in tissue dimensionsresulted in an _v + value of 192 bars for oak. If _v + and rare the same for all cells in the tissue, L_p for the sieve elementsof oak is 9.6 x 10^–8 cm s^–1 bar^–1. Exudationfrom the sieve elements of white ash during excision of thephloem led to artificially high values of _v + for that species. Quercus borealis michx. f., Fraxinus americana var, biltmoreana (Beadle) J. Wright, red oak, white ash, water relations, phloem, volumetric elastic modulus, membrane hydraulic conductivity     

Wilting of Leaves in Vicia faba L.

Wilting of leaves of Vicia faba L., which occurs when the pressurepotential (_p) is zero, and the leaf-water potential () at wiltingboth depend entirely upon the solute potential at incipientplasmolysis (_so) and not on soil-water status. Wilting in V.faba is acropetal; this is consistent with the hypothesis thatthere is a gradient of decreasing _so up the plant and that wateris transferred from the lower to the upper leaves, hasteningthe overall water loss from the lower leaves to the point when_p is zero. The gradient in _so up the plant is of the order of3–8 bar. It is proposed that wilting when _p>0 (i.e. > _so) shouldbe ‘apparent wilting’ and that when _p0 (i.e. _so),‘true wilting’.     

A Transient Stimulation of Net Photosynthesis of Rye Leaves by {alpha}-Hydroxy-2-pyridinemethanesulphonic Acid ({alpha}-HPMS) due to Inhibition of Photorespiratory CO2 Release

The effects of -hydroxy-2-pyridinemethanesulphonic acid (-HPMS)upon net photosynthesis (P_n, the CO₂ compensation point (),post-lower illumination burst of CO₂ (PLIB) and post-lower temperatureburst of CO₂ (PLTB) in detached rye (Secale cereale L.) leaveswere investigated. At low concentrations ( 0.5 mol m^–3),-HPMS initially stimulated P_n and decreased the magnitude ofboth PLIB and PLTB. The decreased at all concentrations of-HPMS (0.05–5.0 mol m^–3. The effects of -HPMS onP_n and were time-dependent and, after a few minutes, the P_nwas inhibited while values increased considerably. At a higherconcentration (5.0 mol m ^–3), the transient effects of-HPMS were shorter () or not observed at all (P_n. Both PLIBand PLTB, when expressed in relation to P_n, increased at higherlevels of this compound. Similar data with respect to the effectsof -HPMS on PLIB and PLTB were found for leaves of dandelion(Taraxacum officinale L.). The results suggest that -HPMS may stimulate P_n by inhibitingphotorespiration, as originally suggested by Zelitch (1966),but only at low concentrations and over a short time span. Thedecrease of PLIB and PLTB values at low -HPMS levels is consistentwith these processes being a residual activity of the glycolatepathway. Key words: CO₂ compensation point, -hydroxy-2-pyridinemethanesulphonic acid, photorespiration, photosynthesis     

Monte Carlo Estimation for Nonlinear Non-Gaussian State Space Models

We develop a proposal or importance density for state spacemodels with a nonlinear non-Gaussian observation vector y p(y¦)and an unobserved linear Gaussian signal vector p(). The proposaldensity is obtained from the Laplace approximation of the smoothingdensity p(¦y). We present efficient algorithms to calculatethe mode of p(¦y) and to sample from the proposal density.The samples can be used for importance sampling and Markov chainMonte Carlo methods. The new results allow the application ofthese methods to state space models where the observation densityp(y¦) is not log-concave. Additional results are presentedthat lead to computationally efficient implementations. We illustratethe methods for the stochastic volatility model with leverage.