Sequence gaps join mice and men: phylogenetic evidence from deletions in two proteins

Recent nuclear sequence analyses have provided evidence thatprimates and rodents are more closely related than previouslybelieved (Madsen et al. 2001 ; Murphy et al. 2001a, 2001b ).This proposal is difficult to reconcile with morphological insights(Liu et al. 2001 ; Novacek 2001 ) and is not generally supportedby current mitochondrial sequence data (Reyes, Pesole, and Saccone2000 ; Nikaido et al. 2001 ; Arnason et al. 2002 ; Janke etal. 2002 ). Moreover, the supporting data and analyses havebeen criticized on methodological grounds (Rosenberg and Kumar2001 ). Here we report deletions in two nuclear protein-codinggenes that lend independent support     

Carbon isotopic composition of Trichodesmium spp. colonies off Bermuda: effects of colony mass and season

Colonies of Trichodesmium spp. are conspicuous, macroscopiccomponents of the life in tropical and subtropical oceans. Thelarge size and the morphology of the colony raise questionsregarding the mechanism of carbon supply for photosynthesis.Constraints on these mechanisms may be indicated by the stablecarbon isotopic composition (¹³C) that reflects the balancebetween carbon supply and speciation, as well as the growthrate and colony size. The ¹³C of Trichodesmium off Bermuda measuredhere revealed a strong correlation between size of individualcolonies and season. The smallest colonies, 2–7 µgC colony^–1, showed the lightest ¹³C composition (–19),increasing to asymptotic values of –12 above 7 µgC colony^–1. The average ¹³C of the colonies was lightestimmediately after the onset of stratification in the SargassoSea, gradually increasing by 4 to heavier values during thesummer. We propose that the mass effect is due to increaseduse of HCO₃^– by the larger colonies, whereas the seasonalinfluence may be related to changes in irradiance and pCO₂ affectingthe internal carbon cycling.     

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.     

Potassium Transport Across the Membranes of Chara: II.42K FLUXES AND THE ELECTRICAL CURRENT AS A FUNCTION OF MEMBRANE VOLTAGE

Smith, J. R. 1987. Potassium transport across the membranesof Chara. II. ⁴²K fluxes and the electrical current as a functionof membrane voltage.—J. exp. Bot. 38: 752–777. The current required to clamp the trans-membrane voltage ofinternodal cells of Chara australis at different levels wasmeasured simultaneously with either the ⁴²K influx or efflux.Examination of the voltage-dependence of the ratio of the electricalcurrent to the unidirectional tracer fluxes yielded no evidenceof any amplification of the electrical driving force on theK⁺ ions. There was thus no evidence for the interaction of K⁺ions with themselves or any other species during their passageacross the membrane. These measurements allow the determinationof , the fraction of the electrical current carried by K⁺ ions.When the external [K⁺] = 10 mol m^–3, the average valueof was 0?85 for V_m > –125 mV and 07?5 for V_m <–150 mV. When the external [K⁺] = 0?1 mol m^–3, was 0?6 for V_m < –80 mV and 0?1 for V_m > –250mV. It was also found that the conductance associated with K⁺transport was inhibited by hyperpolarization. Key words: Potassium, conductance, flux-ratio     

{delta}15N signatures of marine mesozooplankton and seston size fractions in Kiel Fjord, Baltic Sea

The ¹⁵N of marine mesozooplankton species was measured on fouroccasions. Significant differences were found between copepodsand meroplanktonic larvae, yet not between holoplanktonic species.On average, mesozooplankton was enriched by 3.4 ± 0.9relative to selected seston size fractions. Despite suggestingsmall differences (0.5 to 1) in the ¹⁵N of different phytoplanktontaxa on one occasion, the size fractionation procedure generallyproved inadequate in separating major taxonomic groups composingseston. This circumstance, and phase-shifts in the transmissionof rapid changes (>2) in seston ¹⁵N to mesozooplankton complicatethe calculation of mesozooplankton trophic levels.     

Variation in Natural Abundance of 15N among Plant Parts and in 15N/14N Fractionation during N2 Fixation in the Legume-Rhizobia Symbiotic System

Sixteen legumes were grown in N-free media so that N was suppliedentirely by symbiotic N₂ fixation. The plant tissues were analyzedfor natural ¹⁵N abundance (expressed as ¹⁵N per mil relativeto air N₂) with a ratio mass spectrometer. The nodules of desmodium,centro, siratro, soybean and winged bean showed high enrichmentin ¹⁵N (+9), while red clover showed slight enrichment (+2).The nodules of 9 other forage legumes (Townsville stylo, whiteclover, alsike clover, common vetch, Chinese milk vetch, senna,alfalfa, ladino clover, and hairy vetch) showed little enrichmentin ¹⁵N. In all the legumes investigated, particularly in the ureide-transportingplants such as desmodium, centro, siratro, soybean, winged beanand field bean, the ¹⁵N value of the shoots was negative (–3.2).The ¹⁵N value of the shoots in winged bean and field bean variedby about 1 depending on the Rhizobium strains used. The isotopicmass balance of 13 legumes indicated that isotopic fractionationoccurs during N₂ fixation by the legume-rhizobia symbiosis witha preference for ¹⁴N over ¹⁵N, resulting in a ¹⁵N value of –0.2to –2 in the whole plant. The results indicate that ¹⁵N/¹⁴N isotopic discrimination witha preference for the lighter atom may occur in both N₂ fixationand export of fixed N from nodules. ¹Present address: Department of Soils and Fertilizers, NationalAgriculture Research Center, Kannondai, Tsukuba, Ibaraki 305,Japan. (Received October 8, 1985; Accepted April 7, 1986)     

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.     

An Error in the Calibration of Xylem-water Potential against Leaf-water Potential

An error occurs in the calibration of xylem pressure potential() against leaf-water potential () when the calibration is madeusing plant material in which the water stress has been inducedartificially after excision. The impostion of water stress afterexcision affects the determination more than it affects , consequentlythe relationship between these two indices of water stress isaltered. Care should be exercised to ensure that identical proceduresare adopted during . calibrations and during susbsequent fieldmeasurements of with the pressure-chamber apparatus.     

A novel alpha1,2-fucosyltransferase (CE2FT-2) in Caenorhabditis elegans generates H-type 3 glycan structures

The 1,2-fucosyltransferase family (1,2FT) is the largest familyof glycosyltransferases in the genome of the free-living nematodeCaenorhabditis elegans, and early evidence suggests that eachmember may have a unique activity. Here we describe a C. elegansgene (designated CE2FT-2) encoding an 1,2FT that has the potentialto generate the sequence Fuc1-2Galβ1-3GalNAc-R, which isthe H-type 3 blood group structure. The CE2FT-2 cDNA encodesa putative transmembrane protein that shows 42% amino acid identityto a previously cloned C. elegans 1,2FT (termed CE2FT-1), buthas a very low identity (16–20%) to 1,2FT sequences inhumans, rabbits, and mice. A recombinant form of CE2FT-2 expressedin human 293T cells has a high 1,2FT activity toward Galβ1-3GalNAc-O-pNP,but unexpectedly, the enzyme is inactive toward the acceptorGalβ-O-phenyl. Thus, CE2FT-2 differs from all other 1,2FTspreviously described from animals that all utilize Galβ-O-phenyl.CE2FT-2 is expressed at all stages of worm development, butremarkably, promoter analysis of the CE2FT-2 gene using greenfluorescent protein reporter constructs indicates that the CE2FT-2is expressed exclusively in pharyngeal cells of the worm fromembryo to an adult stage. Because pharyngeal cells are knownto secrete their glycoconjugates to the nematode surface, theseresults may indicate that products of CE2FT-2 contribute tointeractions of the nematode with its environment or are usedas ligands for bacterial attachment. These findings, along withthose on other 1,2FTs in C. elegans, suggest that each 1,2FTin this organism may have a unique acceptor specificity, expressionpattern, and biological function.     

The Meaning of Matric Potential

The commonly used equation, = P - + , which describes thepartitioning of plant water potential, , into components ofhydrostatic pressure, P, osmotic pressure, , and matric potential,, is misleading. The term , which is supposed to show the influenceof a solid phase on , is zero if a consistent definition ofpressure is used in the standard thermodynamic derivation. However,it can be usefully defined by = + _D, where _D is the osmoticpressure of the equilibrium dialysate of the system. The practicaland theoretical significance of this definition is discussed.     

Adaptation of the Euryhaline Charophyte Lamprothamnium papulosum to Brackish and Freshwater: Turgor Pressure and Vacuolar Solute Concentrations During Steady-State Culture and After Hypo-osmotic Treatment

The euryhaline charophyte Lamprothamnium papulosum (Wallr.)J. Gr. was adapted to media with decreasing salinities rangingfrom 550 to 0 mosmol kg^–1. Vegetative plants grown inmedia with osmotic pressures (⁰) in the range of 550 to 130mosmol kg^–1 maintained a constant turgor pressure () at309 + 7 mosmol kg^–1. The ions K+, Na+ and Cl–, werethe predominant solutes in the vacuole. Changes in their concentrationsaccount for the variation in internal osmotic pressure (¹) with,⁰. The divalent ions Mg²⁺, Ca²⁺ and were also present in significant amounts, but their concentrationsdid not alter with changes in, ⁰. In cells subjected to hypo-osmotic shock the regulation of was incomplete. The turgor pressure increased from 302 to 383mosmol kg^–1. The first rapid response to the sudden decreasein ⁰ was a loss of K⁺ and Cl^–. In contrast to the decreasein ionic concentrations an accumulation of sucrose occurredwhich could account for the increase of . The increase in sucroseconcentration started 24 to 48 h after the downshock and reachedits highest value after 3 to 4 weeks. The sucrose concentrationin the vacuole was up to 320 mol m^–3. During this timethe ionic content continued to decrease but did not counterbalancethe sucrose concentration sufficiently to regain the original. High sucrose levels accompanied by an enhanced were also observedduring the period of fructification (sexual reproduction: formationof antheridia and oogonia) in Lamprothamnium kept under conditionsof constant salinity. It is concluded that high sucrose content and elevated arecharacteristic of sexual reproduction in this charophyte. Lamprothamniumis able to tolerate different during various developmentalstages (e.g. vegetative and reproductive phases). Key words: Lamprothamnium papulosum, sucrose, turgor pressure     

Molecular dynamics simulations of oligosaccharides and their conformation in the crystal structure of lectin-carbohydrate complex: importance of the torsion angle {psi} for the orientation of {alpha}1,6-arm

The conformation of the heptasaccharide Man-1,6-(Man-1,3)(Xyl-ß1,2)-Man-ß,4-GlcNAc₂-ß1,4-(L-Fuc-1,3)-GlcNAc₁,the carbohydrate moiety of Erythrina corallodendron lectin (EcorL),the hexasaccharide Man-1,6-(Man-1,3) (GlcNAc-ß1,4)-Man-ß1,4-GlcNAc-ß1,4-GlcNAcand their disaccharide fragments have been studied by moleculardynamics (MD) simulations for 1000 ps with different initialconformations. In the isolated heptasaccharide, the most frequentlyaccessed conformation during MD has a value of 180° aroundMan-1,6-Man linkage. This conformation is stabilized by theformation of a hydrogen bond between the carbonyl oxygen ofGlcNAc₂ with the O3/O4 hydroxyls of the 1,6-linked mannose residue.The conformation of the heptasaccharide found in the crystalstructure of the EcorL-lactose complex (Shaanan et al., Science,254, 862, 1991), that has a value of 76° around Man-1,6-Manlinkage, is accessed, although less frequently, during MD ofthe isolated oligosaccharide. The ,, = 58°,–134°,–60°conformation around Man-₁,6-Man fragment observed in the crystalstructure of the Lathyrus ochnrs lectin complexed with a biantennaryoctasaccharide (Table I in Homans,S.W., Glycobiology, 3, 551,1993) has also been accessed in the present MD simulations.These values for the 1,6-linkage, which are observed in theprotein-carbohydrate crystal structures and are accessed inthe MD simulations, though occasionally, have not been predictedfrom NMR studies. Furthermore, these different values of leadto significantly different orientations of the 1,6-arm for thesame value of . This contrasts with the earlier predictionsthat only different values of can bring about significant changesin the orientation of the ₁,6-arm. The MD simulations also showthat the effects of bisecting GlcNAc or ß1,2-xyloseare very similar on the ₁,3-arm and slightly different on the₁,6-arm. bisecting GlcNAc carbohydrates glycoprotein lectinsaccharide complex     

Daily vertical migration of dense deep scattering layers related to the shelf-break area along the northwest coast of Baja California, Mexico

Echo signals were collected with a Simrad 200 kHz transduceracross the shelf-break features off the northwest coast of BajaCalifornia (30°05'–30°42'N, 115°50'–116°26'W)during two diel cycles (July 1995) with the objective of describingvertical migrations of two dense deep scattering layers (DSL)found near the shelf break. DSL records were made within anarea ±50 m in the neritic zone, ±200 m at theshelf break and ±1000 m depth in the offshore station.Using an Isaacs-Kidd midwater net and Bongo nets, we inferredthat the DSL were composed mainly of juveniles and adults ofthe euphausiids Nyctiphanes simplex Hansen and Euphausia pacificaHansen. These aggregations have a close interaction with theocean bottom during the daytime and display a vertical migration,rising near to the surface at night where a progressive horizontaldispersion then occurs. The DSL measured 3.5–6.0 km horizontallyduring the night. The ascent and descent migrations of the DSLwere significantly fitted to a polynomial function of the secondorder, suggesting different swimming behavior during these twoprocesses. Vertical migrations of the DSL were between 60 and90 m. During the descent migration, maximum instantaneous speedsreached 0.7 cm s¹, and during the ascent, maximum instantaneousspeeds were 0.3 cm s¹. These coastal euphausiid species, alongwith other macrozooplankton and nektonic organisms, have a dailyclose interaction with the ocean bottom and also with the pelagicenvironment, suggesting that they play an important role providingfood for demersal and pelagic organisms on the slope and shelfbreak in the upwelling region off the northwest coast of BajaCalifornia.     

Further characterization of the binding properties of a GalNAc specific lectin from Codium fragile subspecies tomentosoides

Previous study on the binding properties of a lectin isolatedfrom Codium fragile subspecies tomentosoides (CFT) indicatesthat this lectin recognizes the GalNAc1 sequence at both reducingand nonreducing ends. In this study, the carbohydrate specificityof CFT was further characterized by quantitative precipitin(QPA) and inhibition of lectin-enzyme binding assays. Of theglycoforms tested for QPA, all asialo-GalNAc1 containing glyco-proteinsreacted well with the lectin. Asialo hamster and ovine submandibularglycoproteins, which contain almost exclusively Tn (GalNAclSer/Thr)residues as carbohydrate side chains, and Streptococcus typeC polysaccharide completely precipitated the lectin added, whilethe GalNAcβcontaining Tamm-Horsfall Sd(a⁺) glycopro-teinand its asialo product were inactive. Among the oligo-saccharidestested for inhibiting lectin-glycoprotein interaction, GalNAc13GalNAcβ13Gal14Galβ14GIc(Fp)and Galβ13GalNAc1benzyl (T) were the best, and about 125-foldmore active than GalNAc They were about 3.3, 6.6, and 43 timesmore active than Tn containing glycopeptides, GalNAc13(LFuc12)Gal(A_h) and Galβ13GalNAc(T), respectively. From the presentand previous results, it is concluded that the combining siteof CFT is probably of a groove type that recognizes from GalNAclto pentasaccharide(Fp). The carbohydrate specificity of thislectin can be constructed and summarized in decreasing orderby lectin determinants as follows: Fp and T > Tn cluster> A_h >>I/II. carbohydrate specificities Codium fragile tomentosoides glycoprotein binding lectins     

Pumpkin (Cucurbita sp.) seed globulin IV. Terminal sequences of the acidic and basic peptide chains and identification of a pyroglutamyl peptide chain

Pumpkin seed globulin is composed of heterogeneous polypeptidechains, acidic and chains and basic ₁ and ₂ chains (12). This study showed that the basicchains had similar N-terminal sequences, Gly-Leu-Asp-Glu-Thr-Ile-for the ₁ chain and Gly-Leu-Glu-Glu-Thr-Ile- for ₂. On the contrary,the N-terminal sequences of the acidic and chains were dissimilar, Ile-Gln-Gly-Tyr- for the chain and no N-terminal residue for the chain, according to routine terminal analysis. Pyrrolidonylpeptidase digestion of the chain and its thermolysin digestion followed by Edman degradationsrevealed that the N-terminal sequence of the chain was < Glu-Ile-Glu-Gln-Gln-Glu-Pro(Trp,Ser)-. The N-terminal sequences and the C-terminal residuesindicated that the acidic and chains were more heterogeneous than the basic ₁ and ₂ chains.A preliminary study on the degradation of storage globulin isalso presented. (Received November 9, 1979; )     

Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila

Natural selection influences synonymous mutations and synonymouscodon usage in many eukaryotes to improve the efficiency oftranslation in highly expressed genes. Recent studies of genecomposition in eukaryotes have shown that codon usage also variesindependently of expression levels, both among genes and atthe intragenic level. Here, we investigate rates of evolution(Ks) and intensity of selection (_s) on synonymous mutationsin two groups of genes that differ greatly in the length oftheir exons, but with equivalent levels of gene expression andrates of crossing-over in Drosophila melanogaster. We estimate_s using patterns of divergence and polymorphism in 50 Drosophilagenes (100 kb of coding sequence) to take into account possiblevariation in mutation trends across the genome, among genesor among codons. We show that genes with long exons exhibithigher Ks and reduced _s compared to genes with short exons.We also show that Ks and _s vary significantly across long exons,with higher Ks and reduced _s in the central region comparedto flanking regions of the same exons, hence indicating thatthe difference between genes with short and long exons can bemostly attributed to the central region of these long exons.Although amino acid composition can also play a significantrole when estimating Ks and _s, our analyses show that the differencesin Ks and _s between genes with short and long exons and acrosslong exons cannot be explained by differences in protein composition.All these results are consistent with the Interference Selection(IS) model that proposes that the Hill-Robertson (HR) effectcaused by many weakly selected mutations has detectable evolutionaryconsequences at the intragenic level in genomes with recombination.Under the IS model, exon size and exon-intron structure influencethe effectiveness of selection, with long exons showing reducedeffectiveness of selection when compared to small exons andthe central region of long exons showing reduced intensity ofselection compared to flanking coding regions. Finally, ourresults further stress the need to consider selection on synonymousmutations and its variation—among and across genes andexons—in studies of protein evolution.     

Pumpkin (Cucurbita sp.) seed globulin III. Comparison of subunit structures among seed globulins of various Cucurbita species and characterization of peptide components

Various Cucurbita seed globulins showed patterns similar toone another on SDS-gel electrophoresis, and ß bandsfor unreduced globulins and , ', and ' bands for reduced ones.On gel electrophoresis in 6 M urea, reduced globulin gave twoacidic and two basic bands. These corresponded to and ' chainsand ₁ and ₂ chains, respectively, identified by two-dimensionalurea-SDS gel electrophoresis. The compositions of the and ßsubunits were proposed. (Received September 8, 1977; )     

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     

Isolation of Subunits of Coupling Factor 1 from Maize and Spinach Chloroplasts and Properties of Combinations of Subunits with ATPase Activity

Subunits (, ß, ) and mixtures of subunits ( ß, , ß , ß ) were isolated without denaturationfrom a chloroform extract of chloroplast coupling factor 1 (CF₁)from maize (Zea mays var. Ushiku 5-4) and from spinach by fastprotein liquid chromatography (FPLC), on an anion-exchange columnof Mono-Q in the presence of n-octylglucoside (OG) and on achromatofocusing column of Mono-P. The ß -subunitcomplex (CF¹ ß ) was the minimum unit required forATPase activity, as was confirmed by the reconstituted complexof ß and subunits. An subunit isolated from maizeinhibited the ATPase activity of CF₁ ß from bothmaize and spinach. CF₁ ß was found to contain anOG-dependent Mg²⁺-ATPase. The ATPase activity of CF₁ ß required divalent cations, such as Mg²⁺ or Mn²⁺, for its expressionin the presence of OG; its optimum pH was 8.0 and it was markedlyinhibited by NaN₃. The enzyme hydrolyzed ATP in prefernece toGTP but not CTP, UTP, ADP, AMP or pNPP. Lineweaver-Burk plotsof its activity were curvilinear in the range of 0.6–0.7mM ATP.Mg²⁺. ¹Present address: Department of Biology, School of Education,Waseda University, Shinjuku-ku, Tokyo, 160 Japan. (Received February 15, 1989; Accepted April 20, 1989)