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.     

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.     

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.     

A Novel Method for Generating Nested Deletions Using the in Vitro Bacteriophage T3 DNA Packaging System

To sequence a DNA segment inserted into a cosmid vector underthe directed sequencing strategy, we established a simple andrapid method for generating nested deletions which uses thein vitro packaging system of bacteriophage T3 DNA. The principleis based on the previous finding that this system can translocateany linear double-stranded DNA up to 40 kb into the phage capsidin a time-dependent manner and the encapsulated DNA becomesDNase-resistant. For this purpose, we constructed a cosmid vectorthat carries two different antibiotic selection markers at bothsides of the multiple cloning site, and after insertion of aDNA segment, the clone was linearized by -terminase at the cossite. After the packaging reaction in vitro followed by DNasetreatment, the encapsulated DNA was introduced into Escherichiacoli cells to give clones with unidirectional deletions by differentialantibiotic selection. Restriction and sequence analyses of deletionclones demonstrated that an ordered set of clones with nesteddeletions, ranging from less than 1 kb to 25 kb, was createdfrom either the end of the DNA segment. Thus, nested deletionclones that cover the entire region of a 40-kb cosmid insertcan be obtained by a single packaging reaction, and its restrictionmap can be simultaneously obtained.     

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.     

An NTP-Binding Protein That Cross with a Ras-Specific Antibody in the Myceia of Neurospora crassa

A Ras-related NTP-binding protein was partially purified froma membrane fraction derived from the mycelia of Neurospora crassa.[-³²P]ATP and [-³²P]GTP were incubated with mem brane and solublefractions which were then irradiated with UV light to inducecrosslinking of tightly bound nucleotides. After SDS-polyacrylamidegel electrophoresis, blotting onto a nitrocellulose filter andautoradiography it was apparent that most of the proteins thatbound [-³²P]-GTP also bound [-³²P]ATP. Pretreatment of the membranefraction with Ras-specific antibody effectively blocked thebinding of [-³²P]ATP and [-³²P]GTP to several ATP-GTP-bindingproteins. The band of a protein with a molecular weight of 26kDa on the SDS-polyacrylamide gel cross-reacted strongly withthe Ras-specific antibody. The protein was extracted from thegel and further purified by repeated gel electrophoresis. Thepurified protein bound [-³²P]ATP, [-³²P]-GTP, [-³²P]CTP and[-³²P]UTP at 1.6x10^– M and was autophosphorylated in thepresence of [-³²P]ATP and [-³²P]GTP at 1.7x10 M. Pretreatmentof the protein with Ras-specific antibody partially blockedthe autophosphorylation in the presence of these nucleotides.The binding of [-³²P]ATP to the NTP-binding protein was blockedby addition of ATP at 10^–4–10^–3 M. ATP ata concentration of 10^–4 M prevented the binding of [-³²P]to a greater extent than did GTP at the same concentration.Binding of [-³²P]CTP and [-³²P]UTP to the protein was also observed. (Received October 7, 1991; Accepted July 14, 1992)     

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     

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.     

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     

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’.     

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     

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, .     

Alternative Methods of Analysing Water Potential Isotherms: Some Cautions and Clarifications: I. THE IMPACT OF NON-IDEALITY AND OF SOME EXPERIMENTAL ERRORS

In recent years alternative ways have been proposed to transformmeasurements of leaf water potential, , and relative water content,R^*, in order to derive values of osmotic pressure at full turgidityin leaves and shoots, ^o(when 0). Two types of transformationsare usually considered: 1/ versus R^* and versus 1/R^*, and linearregression is used to fit the data in the region where turgoris thought to be zero. It appears that when ^o is estimated bylinear extrapolation of 1/Psi; versus R^* then apoplastic watermight not influence the accuracy of ^o but when the versus \/R^*transformation is used apoplastic water causes an underestimateof ^o. We examine the accuracy of the estimate of ^o obtainedfrom the two transformations when there are random errors in, systematic errors in , and when the osmotic solutions arenon-ideal. The 1/ versus R^* transformation generally producesthe best estimate of ⁰ by linear extrapolation.     

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     

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     

A novel monoantennary complex-type sugar chain found in octopus rhodopsin: occurrence of the Gal{beta}1->4Fuc group linked to the proximal N-acetylglucosaniine residue of the trimannosyl core

The N-linked sugar chains were liberated as oligosaccha-ridesfrom octopus rhodopsin by hydrazinolysis. Most of the oligosaccharideswere neutral, and separated into two major components by columnchromatography using immobilized lectins and Bio-Gel P-4. Structuralanalysis of the one major component by sequential exoglycosidasedigestion, chemical fragmentation in combination with meth-ylationanalysis revealed that it is a nonasaccharide; Man16(Gaiβ13GlcNAcβ12Man13)Manβ14GlcNAcβ14(Galβ14Fuc16)GlcNAcThis structure is quite unique in that a novel galactosylatedfucose residue is attached to the reducing terminal N-acetyl-glucosamineresidue. galactosylated Fuc N-linked sugar chain novel structure octopus rhodopsin     

Stomatal Behaviour and Water Relations of Chilled Phaseolus vulgaris L. and Pisum sativum L.

Leaf diffusion resistance interpreted as stomatal resistance,leaf water potential (_w), solute potential (_s) and leaf turgorpotential (_p) of the chilling sensitive species Phaseolus vulgariswere determined during chilling at 4 °C in the light. Bothchill-hardened and non-hardened plants were used. For comparison,the chilling resistant species Pisum sativum was also used. The results for chilled P. sativum were similar to those obtainedfor chill-hardened P. vulgaris plants receiving a chilling treatment.In both cases a reduction in stomatal aperture and the maintenanceof a positive leaf turgor were the responses to chilling. Leavesof chilled but non-hardened P. vulgaris plants were found tomaintain open stomata throughout the chilling treatment despitea severe wilt developing after 7 h at 4 °C. This was incontrast to the chill-resistant P. sativum. which showed a rapidclosing and subsequent re-opening of the stomata to a new reducedaperture. During the first 12 h of chilling _wof P. vulgaris leaves changedfrom –0.47 MPa to –1.24 MPa. On more prolonged chilling_w tended to return to pre-chilling values. In addition. _p decreasedfrom 0.42 MPa to zero after only 9 h of chilling, and remainedat this value for the remainder of the chilling period, _s, changedrapidly from –0.89 MPa to –1.35 MPa in the first7.5 h, and after 9 h. _w and _s, were equal, i.e. zero _p. In contrast,the chilling resistant plant P. sativum maintained a positive_p throughout the chilling period, and there was little differencebetween values of _w, and _s in control and chilled leaves. Key words: Chilling, Stomata, ater relations, Phaseolus vulgaris, Pisum sativum