CORRIGENDA

M. I. BAXTER and R. H. NISBET. Features of the nervous systemand heart of Archachatina revealed by the electron microscopeand by electrophysiological recording. Proc. malac. Soc. Lond.35, 167–177. p. 169, line 3. For (Amoroso et al., 1953) read (Amoroso etal., 1963). p. 176, References 1 and 2. For (In press) read (In preparation). Plates 18 to 31. Read magnification of Plate 18 as x 4200, andthat of remaining plates to nearest 1000.     

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.     

Effect of photoinhibition on algal photosynthesis: a dynamic model

Recent evidence from algal physiology and molecular biologyconfirms that photoinhibition is directly related to D1 proteindamage and recovery, and D1 protein damage leads to a decreasein electron transfer or an increase in turnover time of theelectron transfer chain. In this study, the turnover time ofthe electron transfer chain is defined as a function of therelative concentration of D1 protein in reaction centre II andthe photoinhibition processes due to D1 protein degradationare incorporated into a model of photosynthesis, initiated byDubinsky et al. (Plant Cell Physiol., 27, 1335–1349, 1986)and developed by Sakshaug et al. (Limnol. Oceanogr., 34, 198–205,1989). D1 protein damage is assumed to be both light and D1protein concentration dependent, and to be proportional to thecross-section of PSII (     

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.     

Structural studies on the tri- and tetrasaccharides isolated from porcine intestinal heparin and characterization of heparinase/heparitinases using them as substrates

We prepared a series of oligosaccharides from porcine intestinalheparin after extensive digestion with a mixture of Flavobacteriumheparinase as well as heparitinases I and II. Previously, wereported the structures of the two glycoserines derived fromthe carbohydrate-protein linkage region [Sugahara et al., J.Biol. Chem., 267, 1528–1533 (1992)] and three tetrasaccharidesderived from the antithrombin III-binding site [Yamada et al.,J. Biol. Chem., 268, 4780–4787 (1993)]. In this study,we determined the structures of 10 other tetrasaccharides anda trisaccharide by enzymatic digestion, fast atom bombardmentmass spectrometry and 500-MHz ¹H NMR spectroscopy. These tetrasaccharidesshare the common disulphated structure,     

ERRATUM

R. MANLY. The larval development of Tricolia pullus (L.)J. moll.Stud. (1976) 42,361–369. The legends of Figs 2 and 3 shouldbe transposed.     

Growth and decline of a diatom spring bloom phytoplankton species composition, formation of marine snow and the role of heterotrophic dinoflagellates

During the spring of 1994, we determined the factors responsiblefor the decline of the seasonal diatom bloom in the Gullmarfjord, on the west coast of Sweden. Four species constituted>75% of the biomass—Detonula confervacea, Chaetocerosdiadema, Skeletonema costatum and Thalassiosira nordenskioeldii—reachingconcentrations of 4900, 350, 8200 and 270 cells ml^–1,respectively. Growth of phytoplankton was exponential (growthrate = 0.12 day^–1) from 3 to 21 March, after which a galewith winds >15 m s^–1 caused massive aggregation. Amaximum of 130 p.p.m. (v/v) of marine snow aggregates was observedby in situ video at the peak of the bloom. Critical concentrations(Jackson, Deep-Sea Res., 37, 1197–1211, 1990) were similarto observed showing that coagulation theory could explain thesudden decline of the bloom. The heterotrophic dinoflagellateGyrodinium cf. spirale increased exponentially after the peakof the bloom with maximum (temperature-adjusted) growth rates.After the rapid aggregation and sedimentation of the bloom,they were able to control any further growth of diatoms. Nitrateand silicate were never depleted, but phosphate may have beenlimiting by the end of the study period. We conclude that massaggregation during a gale marked the end of the bloom, and thatintense grazing by heterotrophic dinoflagellates prevented anysubsequent increase of diatoms.     

Evolution of the Replication Regions of IncI{alpha} and IncFII Plasmids by Exchanging Their Replication Control Systems

The basic replicons of bacterial plasmids consist of two setsof genetic systems, the replication-structural system and thereplication control system. Comparison of nucleotide sequencessuggested that the basic replicons of plasmids P307 (IncFI)and pMU2200 (IncZ) were generated by reciprocal recombinationbetween ancestors of R100 (IncFII) and ColIb-P9 (IncI), or viceversa. The plasmids of each pair, P307/pMU2200 and R100/ColIb-P9,are structurally unrelated to each other. Based on this information,we constructed in vitro and analyzed P307-like chimeric repliconsfrom ColIb-P9 and R100. When the replication-structural regionof ColIb-P9 was combined with the whole replication controlregion of R100, the resultant replicon replicated stably asR100 did. These results revealed that the basic replicons ofthe plasmids diverged by exchanging their replication controlsystems. Thus, we propose that the replication control systemsof plasmids, in some cases, evolved independently of their structuralsystems, although these two systems work together to maintainthe replication functions. We also showed that the reciprocalrecombination was specified by the unique secondary structuresof RNA involved in the control of expression of the genes encodingthe replication initiator proteins.     

Time course of recovery from nerve injury in skeletal muscle: energy state and local circulation

Hayashi, Yoshihiro, Takaaki Ikata, Hiroaki Takai, ShinjiroTakata, Takayuki Sogabe, and Keiko Koga. Time course of recoveryfrom nerve injury in skeletal muscle: energy state and localcirculation. J. Appl. Physiol. 82(3):732-737, 1997.This study examined the time course of recoveryfrom nerve injury on energy state assessed by phosphorus-31 magneticresonance spectroscopy and local circulation dynamics by fluorine-19magnetic resonance spectroscopy in skeletal muscles ofrats. The hindlimb muscles that had undergone unilateralsciatic nerve compression for 2 wk (CN) were compared withsham-operated (SO) muscles and with muscles that had the compressionremoved after 2 wk and were allowed to recover for 4 wk (R4) or for 6 wk (R6). The energy state and local circulation dynamics of CN muscleswere less than those of SO muscles (P < 0.01). The energy state of R4 muscles remained at levels similar toCN muscles, whereas the local circulation dynamics improved but notback to SO values. In R6 muscles, both parameters returned to SOvalues. These results showed that the recovery processes of circulationprecede those of energy state in skeletal muscles.

     

贵州白山羊Bmp15和Gdf9基因多态性及其编码蛋白的进化分析(英文)

BMP15和GDF9是转化生长因子β（TGFβ）超家族的成员,对绵羊的繁殖性状有直接的调节作用,从中发现的多个高产突变位点直接提高了排卵数和产羔数。在之前的研究中,作者从贵州白山羊中找到了一个高产突变位点。为了进一步揭示Bmp15和Gdf9基因突变与繁殖性状之间的关系,对贵州白山羊Bmp15和Gdf9基因编码区进行了克隆,以人BMP7的晶体结构为模板构建了贵州白山羊BMP15和GDF9成熟肽的三维模型。贵州白山羊Bmp15和Gdf9基因分别编码394和453个氨基酸的蛋白前体。对BMP15和GDF9成熟肽序列进行分析发现,除了之前确认的BMP15中的FecX^B 突变（S99I）和GDF9中的V79I突变之外,还从贵州白山羊的BMP15和GDF9成熟肽分别发现7个和3个位点突变。其中,BMP15成熟肽的S32G、N66H、S99I/P99I和G107R突变可能影响二聚体与受体的结合;GDF9成熟肽的P78Q和V79I影响二聚体与I型受体的亲和力,将值得进一步深入研究。对Bmp15和Gdf9基因编码的蛋白前体序列进行聚类分析,结果显示在鱼类到哺乳类的进化过程中,BMP15出现长度逐渐增加的现象,以BMP15成熟肽N端长度增加为主。这种演变可能使BMP15对低排卵哺乳动物繁殖力的控制更为灵敏。该文的研究结果为贵州白山羊Bmp15和Gdf9基因变异与繁殖力的关系提出了合理的解释,并支持这两个因子是贵州白山羊高产性状重要调节因子的观点。     

Assessment of regional deposition of inhaled particles in human lungs by serial bolus delivery method

Kim, Chong S., S. C. Hu, P. DeWitt, and T. R. Gerrity.Assessment of regional deposition of inhaled particles in human lungs by serial bolus delivery method. J. Appl.Physiol. 81(5): 2203-2213, 1996.Detailedregional deposition of inhaled particles was investigated in youngadults (n = 11) by use of aserial bolus aerosol delivery technique. A small bolus (45 mlhalf-width) of monodisperse aerosols [1-, 3-, and5-µm particle diameter(D_p)] wasdelivered sequentially to a specific volumetric depth of the lung(100-500 ml in 50-ml increments), while the subject inhaled cleanair via a laser aerosol photometer (25-ml dead volume) with a constantflow rate ( = 150, 250, and 500 ml/s) andexhaled with the same without a pause to theresidual volume. Deposition efficiency (LDE) and deposition fraction in10 local volumetric regions and total deposition fraction of the lungwere obtained. LDE increased monotonically with increasing lung depthfor all three D_p.LDE was greater with smaller values in all lungregions. Deposition was distributed fairly evenly throughout the lungregions with a tendency for an enhancement in the distal lung regions for D_p = 1 µm.Deposition distribution was highly uneven forD_p = 3 and 5 µm, and the region of the peak deposition shifted toward the proximalregions with increasingD_p. Surface dosewas 1-5 times greater in the small airway regions and 2-17times greater in the large airway regions than in the alveolar regions.The results suggest that local or regional enhancement of deposition occurs in healthy subjects and that the local enhancement can be animportant factor in health risk assessment of inhaled particles.

     

The duration of copepod life stages estimated from stage-frequency data

Current methods to determine the stage duration of copepodsfrom stage-frequency dataare often based on inappropriate distributionfunctions of the stage development time; they also lack a clearprobability model that describes the random noise in the data.This study aims to estimate the duration of copepod life stages,using an asymmetrical probability distribution function of developmenttime. Data on stage frequency were collected from cultured cohortsof Acartia clausi, Temora longicornis and Pseudocalanus elongatus.In addition, data from cultures of Calanoides carinatus andCalanus australis by Peterson and Painting (J. Plankton Res.,12, 283–293, 1990) were used. Following Landry(Limnol.Oceanogr., 20, 854–858, 1975), for each stage the numberof animals that did not yet pass that stage was plotted as afunction of time. A gamma distribution function appeared todescribe the expected proportion of these animals versus time.The number of animals is assumed to follow a binomial distributionand the model parameters are estimated by maximizing the likelihood.This method enables individuals with a retarded development,which are usually deleted from the data material, to be dealtwith. The median development time was estimated from the gammadistribution functions, from which the duration of the stageswas derived. Isochronal development was confirmed for most stages.However, the first feeding naupliar stage, as well as the lastcopepodite stage (CV), took longer in most species, whereasthe pre-feeding naupliar stages had a shorter duration, particularlyin P.elongatus. Differences betweensexes were not apparent.Contradicting results among cultures and with published resultsbyother workers suggest that part of the observed deviation fromnear-isochronal development may be due to the culture conditions.     

Subsurface phytoplankton blooms fuel pelagic production in the North Sea

The seasonal phytoplankton biomass distribution pattern in stratifiedtemperate marine waters is traditionally depicted as consistingof spring and autumn blooms. The energy source supporting pelagicsummer production is believed to be the spring bloom. However,the spring bloom disappears relatively quickly from the watercolumn and a large proportion of the material sedimenting tothe bottom following the spring bloom is often comprised ofintact phytoplankton cells. Thus, it is easy to argue that thespring bloom is fueling the energy demands of the benthos, butmore difficult to argue convincingly that energy fixed duringthe spring bloom is fueling the pelagic production occurringduring summer months. We argue here that periodic phytoplanktonblooms are occurring during the summer in the North Sea at depthsof >25 m and that the accumulated new production [sensu (Dugdaleand Goering, Limnol. Oceanogr., 12, 196–206, 1967)] occurringin these blooms may be greater than that occurring in the springbloom in the same regions. Thus, such blooms may explain apparentdiscrepancies in production yields between different temperatemarine systems.     

Effect of prior O2 breathing on ventilatory response to sustained isocapnic hypoxia in adult humans

Honda, Y., H. Tani, A. Masuda, T. Kobayashi, T. Nishino, H. Kimura, S. Masuyama, and T. Kuriyama. Effect of priorO₂ breathing on ventilatoryresponse to sustained isocapnic hypoxia in adult humans.J. Appl. Physiol. 81(4):1627-1632, 1996.Sixteen healthy volunteers breathed 100%O₂ or room air for 10 min in random order, then their ventilatory response to sustained normocapnic hypoxia (80% arterial O₂saturation, as measured with a pulse oximeter) was studied for 20 min.In addition, to detect agents possibly responsible for the respiratorychanges, blood plasma of 10 of the 16 subjects was chemically analyzed.1) Preliminary O₂ breathing uniformly andsubstantially augmented hypoxic ventilatory responses.2) However, the profile ofventilatory response in terms of relative magnitude, i.e., biphasichypoxic ventilatory depression, remained nearly unchanged.3) Augmented ventilatory incrementby prior O₂ breathing wassignificantly correlated with increment in the plasma glutamine level.We conclude that preliminary O₂administration enhances hypoxic ventilatory response without affectingthe biphasic response pattern and speculate that the excitatory aminoacid neurotransmitter glutamate, possibly derived from augmentedglutamine, may, at least in part, play a role in this ventilatoryenhancement.

     

Air entry in infant resuscitation: oral or nasal routes?

Wilson-Davis, S. L., S. L. Tonkin, and T. R. Gunn. Air entry in infant resuscitation: oral ornasal routes?. J. Appl. Physiol.82(1): 152-155, 1997.The current recommendation for resuscitation of infants is to blow air into both the nose and mouth.We have observed that mothers cannot cover both the nose and mouth oftheir infants. We compared postmortem tracheal and esophageal air entryby using the nose, combined nose and mouth, and mouth routes in eightinfants. Air entry into the trachea occurred at lower pressures(P < 0.05) via a nose mask than via a combined nose and mouth mask or via a mouth mask. Air entry into thetrachea occurred at lower pressures (P < 0.05) via the nose route in the neutral and extended neck positionscompared with the flexed position. We were unable to demonstrate aneffect of the route of air entry on esophageal air entry. The findings indicate that the nasal route of air entry is more effective than thecombined nose and mouth or mouth routes and that neck flexion impedesair entry. We recommend that parents are taught to blow air into theirinfants' noses if the infant stops breathing.

     

Unequal group variances in microarray data analyses

Motivation: In searching for differentially expressed (DE) genesin microarray data, we often observe a fraction of the genesto have unequal variability between groups. This is not an issuein large samples, where a valid test exists that uses individualvariances separately. The problem arises in the small-samplesetting, where the approximately valid Welch test lacks sensitivity,while the more sensitive moderated t-test assumes equal variance. Methods: We introduce a moderated Welch test (MWT) that allowsunequal variance between groups. It is based on (i) weightingof pooled and unpooled standard errors and (ii) improved estimationof the gene-level variance that exploits the information fromacross the genes. Results: When a non-trivial proportion of genes has unequalvariability, false discovery rate (FDR) estimates based on thestandard t and moderated t-tests are often too optimistic, whilethe standard Welch test has low sensitivity. The MWT is shownto (i) perform better than the standard t, the standard Welchand the moderated t-tests when the variances are unequal betweengroups and (ii) perform similarly to the moderated t, and betterthan the standard t and Welch tests when the group variancesare equal. These results mean that MWT is more reliable thanother existing tests over wider range of data conditions. Availability: R package to perform MWT is available at http://www.meb.ki.se/~yudpaw Contact: yudi.pawitan{at}ki.se Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Martin Bishop     

Temporal dynamics of acute isovolume bronchoconstriction in the rat

Bates, Jason H. T., Thomas F. Schuessler, Carrie Dolman, andDavid H. Eidelman. Temporal dynamics of acute isovolume bronchoconstriction in the rat. J. Appl.Physiol. 82(1): 55-62, 1997.The time course oflung impedance changes after intravenous injection of bronchial agonisthave produced significant insights into the mechanisms ofbronchoconstriction in the dog (J. H. T. Bates, A.-M. Lauzon, G. S. Dechman, G. N. Maksym, and T. F. Shuessler. J. Appl.Physiol. 76: 616-626, 1994). We studied the timecourse of acute induced bronchoconstriction in five anesthetizedparalyzed open-chest rats injected intravenously with a bolus ofmethacholine. For the 16 s immediately after injection, we held thelung volume constant while applying small-amplitude flow oscillationsat 1.48, 5.45, and 19.69 Hz simultaneously, which provided us withcontinuous estimates of lung resistance(RL) and elastance(EL) at eachfrequency. This procedure was repeated at initial lung inflationpressures of 0.2, 0.4, and 0.6 kPa. BothRL andEL increased progressively aftermethacholine administration; however, the rate of change ofEL increased dramatically asfrequency was increased, whereas RL remained relativelyindependent of frequency. We interpret these findings in terms of athree-compartment model of the rat lung, featuring two parallelalveolar compartments feeding into a central airway compartment. Modelsimulations support the notions that both central airway shunting andregional ventilation inhomogeneity developed to a significant degree inour constricted rats. We also found that the rates of increase in bothRL andEL were greatly enhanced as theinitial lung inflation pressure was reduced, in accord with the notionthat parenchymal tethering is an important mechanism limiting theextent to which airways can narrow when their smooth muscle isstimulated to contract.

     

Transformation of Solarium and Nicotiana Species using an Ri Plasmid Vector

Davey, M. R., Mulligan, B. J., Gartland, K. M. A., Peel, E.,Sargent, A. W. and Morgan, A. J. 1987. Transformation of Solanumand Nicotiana species using an Ri plasmid vector.—J. exp.Bot. 38: 1507–1516. Five Nicotiana species (N. benthemiana, N. debneyi, N. occidentals,N. plumbaginifolia, N. tabacum) and three Solanum species (S.dulcamara, S. nigrum, S. tuberosum) were transformed by wild-typeand engineered Ri plasmids. Depending on the host plant, rootstransformed by Agrobacterium strain A4TIII with an Ri plasmidcarrying a chimaeric nopaline synthase-kanamycin resistancegene, were 3 to 40 times more resistant to kanamycin than rootstransformed by the wild-type plasmid of strain A4T. Similarly,plants regenerated from A4TIII-derived roots of N. debneyi,N. plumbaginifolia and N. tabacum were 8 to 16 times more resistantthan A4T plants, and survived at 400 µg cm³ of kanamycin.A4TIII plants of S. nigrum flowered in vitro at 600–1000µg cm³ of kanamycin. Transformed roots and most regeneratedplants synthesized Ri-speciflc opines, while DNA hybridizationconfirmed the presence of DNA homologous to that from wild-typeand engineered Ri plasmids in transformed plants of S. nigrum. Key words: Agrobacterium, Ri plasmid, transformed roots, plant regeneration, kanamycin resistance.