DNA barcoding of Cymbidium by genome skimming: Call for next-generation nuclear barcodes

Cymbidium is an orchid genus that has undergone rapid radiation and has high ornamental, economic, ecological and cultural importance, but its classification based on morphology is controversial. The plastid genome (plastome), as an extension of plant standard DNA barcodes, has been widely used as a potential molecular marker for identifying recently diverged species or complicated plant groups. In this study, we newly generated 237 plastomes of 50 species (at least two individuals per species) by genome skimming, covering 71.4% of members of the genus Cymbidium. Sequence-based analyses (barcoding gaps and automatic barcode gap discovery) and tree-based analyses (maximum likelihood, Bayesian inference and multirate Poisson tree processes model) were conducted for species identification of Cymbidium. Our work provides a comprehensive DNA barcode reference library for Cymbidium species identification. The results show that compared with standard DNA barcodes (rbcL + matK) as well as the plastid trnH-psbA, the species identification rate of the plastome increased moderately from 58% to 68%. At the same time, we propose an optimized identification strategy for Cymbidium species. The plastome cannot completely resolve the species identification of Cymbidium, the main reasons being incomplete lineage sorting, artificial cultivation, natural hybridization and chloroplast capture. To further explore the potential use of nuclear data in identifying species, the Skmer method was adopted and the identification rate increased to 72%. It appears that nuclear genome data have a vital role in species identification and are expected to be used as next-generation nuclear barcodes.     

Production of l-Threonine by Auxotrophic Mutants of Escherichia coli

Two auxotrophic mutants of Escherichia coli have been shown to accumulate significant amounts of l-threonine in the culture medium. One mutant, 13071, is deficient in α,ε-diaminopimelic acid (DAP), and the other, 13070, is deficient in both DAP and methionine.     

The Fine Structure of Nerve Cells and Fibers, Neuroglia, and Sheaths of the Ganglion Chain in the Cockroach (Periplaneta americana)

The abdominal nerve cord of Periplaneta americana was studied utilizing light and electron microscopes. In the nerve cells, delicate granules, similar to those probably responsible for cytoplasmic basophilia, are evenly distributed in "dark" cells and clumped in "light" cells. Neuroglial cells are stained metachromatically by cresyl violet. The neuroglial cells have many processes which ramify extensively and are enmeshed to form overlapping layers. These imbricated processes ensheath the nerve cells; the inner layer of the sheath penetrates into the neuron and is responsible for the appearance of the trophospongium of Holmgren. Nerve fibers are embedded within glial cells and surrounded by extensions of the plasma membrane similar to mesaxons. Depending on their size, two or several nerve fibers may share a single glial cell. Nerve fibers near their terminations on other nerve fibers contain particles and numerous, large mitochondria. The ganglion is ensheathed by a thick feltwork of connective tissue and perilemmal cells. The abdominal connective has a thinner connective tissue sheath which is without perilemmal cells. The nerve fibers and sheaths in the connective become thinner as they pass through ganglia.     

N-Glycan structures of squid rhodopsin.

To determine the glycoforms of squid rhodopsin, N-glycans were released by glycoamidase A digestion, reductively aminated with 2-aminopyridine, and then subjected to 2D HPLC analysis [Takahashi, N., Nakagawa, H., Fujikawa, K., Kawamura, Y. & Tomiya, N. (1995) Anal. Biochem.226, 139-146]. The major glycans of squid rhodopsin were shown to possess the alpha1-3 and alpha1-6 difucosylated innermost GlcNAc residue found in glycoproteins produced by insects and helminths. By combined use of 2D HPLC, electrospray ionization-mass spectrometry and permethylation and gas chromatography-electron ionization mass spectrometry analyses, it was revealed that most (85%) of the N-glycans exhibit the novel structure Manalpha1-6(Manalpha1-3)Manbeta1-4GlcNAcbeta1-4(Galbeta1-4Fucalpha1-6)(Fucalpha1-3)GlcNAc.     

Low root zone temperature favours shoot B partitioning into young leaves of oilseed rape (Brassica napus)

In previous studies with tropical plant species, low root zone temperature (RZT) induced boron (B) deficiency, but it is not known if the same response to RZT will be expressed in temperate species, like oilseed rape, that are more tolerant of low temperature. The present experiments investigated the effect of RZT (10 and 20°C) on oilseed rape ( Brassica napus L. cv. Hyola 42) response to B in solution culture, in summer and winter. Regardless of canopy growth conditions, low RZT (10°C) promoted the partitioning of shoot B to the actively growing leaves, especially when B supply was low. However, low RZT did not significantly alter net B uptake rates or plant biomass. Low RZT decreased the shoot-to-root ratio, countering the effects of low B which increased it, leading to a decreased demand for B in the shoot at low RZT. At low B supply, B-deficiency symptoms appeared later at 10 than at 20°C, corresponding with higher B concentrations in the youngest fully opened leaves (YOLs) at 10°C RZT. Thus 10°C RZT increased the tolerance to low B supply. As a result, it is concluded that the effect of decreasing RZT on the responses of the temperate species, oilseed rape, to low B supply depends on whether the low RZT is above or below the optimal root temperature for growth.     

Production of chitinolytic enzymes from a novel species ofAeromonas

A bacterial strain secreting potent chitinolytic activity was isolated from shrimp-pond water by enrichment culture using colloidal crab-shell chitin as the major carbon source. The isolated bacterium, designated asAeromonas sp No. 16 exhibited a rod-like morphology with a polar flagellum. Under optimal culture conditions in 500-ml shaker flasks, it produced a chitinolytic activity of 1.4 U ml^–1. A slightly higher enzymatic activity of 1.5 U ml^–1 was obtained when cultivation was carried out in a 5-liter jar fermentor using a medium containing crystalline chitin as the carbon source. The secretion of the enzyme(s) was stimulated by several organic nitrogenous supplements. Most carbon sources tested (glucose, maltose, N-acetylglucosamine, etc) enhanced cell growth, but they slightly inhibited enzyme secretion. Glucosamine (0.5% w/v) severely inhibited cell growth (16% of the control), but it did not significantly affect enzyme secretion. The production of chitinolytic enzymes was pH sensitive and was enhanced by increasing the concentration of colloidal chitin to 1.5%. The observed chitinolytic activity could be attributed to the presence of -N-acetylglucosaminidase and chitinase. Chitinase was purified by ammonium sulfate fractionation and preparative gel electrophoresis to three major bands on SDS-PAGE. An in-gel enzymatic activity assay indicated that all three bands possessed chitinase activity. Analysis of the enzymatic products indicated that the purified enzyme(s) hydrolyzed colloidal chitin predominantly to N,N-diacetyl-chitobiose and, to a much lesser extent, the mono-, tri, and tetramer of N-acetylglucosamine, suggesting that they are mainly endochitinases.     

Cigarette advertising and onset of smoking in children: questionnaire survey.

OBJECTIVE: To investigate uptake of smoking in a cohort of 11 to 12 year olds related to awareness of advertised cigarette brands named. DESIGN: Self completed questionnaires administered to whole classes of schoolchildren in June 1993 and June 1994. SETTING: Primary, middle, and secondary schools in the north and south of England. SUBJECTS: 1450 pupils aged 11 and 12 years at the time of the first survey. MAIN OUTCOME MEASURES: Onset of smoking and brands smoked by the second survey related to cigarette brands named in the first one. Less advertised brands were used as the base for calculating odds ratios. RESULTS: Girls who named the most advertised brands-namely, Benson and Hedges alone (odds ratio = 2.50, 95% confidence interval = 1.18 to 5.30) or Benson and Hedges and Silk Cut (2.15, 1.04 to 4.42) in the first survey were at greatest risk of taking up smoking by the second one. The difference was similar but not significant for boys. Boys and girls who named the least advertised brands in the first survey were at no greater risk of taking up smoking by the second survey than those who named no brands (boys odds ratio = 0.49 (0.24 to 1.01); girls 0.79 (0.38 to 1.62)). New smokers were more likely to smoke any available brand (29.5%) or a less advertised brand such as Embassy (24.6%) than the most advertised ones, Benson and Hedges (19.7%) and Silk Cut (14.8%). Established smokers were more selective, only 15% smoking any available brand and 38.3% smoking Benson and Hedges. CONCLUSIONS: Cigarette advertising appears to increase children''s awareness of smoking at a generic level and encourages them to take up the behaviour, beginning with any cigarettes which are available and affordable.     

DISCOVERY OF VERTEBRATE FOSSILS AND PALEOLITHIC ARTIFACTS IN DANJIANG SUBMERGING AREA AND ITS IMPLICATIONS

IntheareatobefloodedinthesecondengineeringstagefortheDanjiangreservoir,wediscovered16vertebratefossillocalitiesand52Paleolithicsitesin1994,andcollected603artifactsandmanyfossils.Ofthel6new1yfoundvertebratefossillocalities,threearereptilesitesrepresentedbydinosaureggsandlimbbones,andl3producemamma1s,including4Pale0gene,2Ne0geneand7Quaternarysites'ThemammalianlocalitiesareofPale0cene,Eocene,EarlyMiocene,andPli0ceneorEarlyPleistocene,MiddleandIntePleistocene,respectively.Theyfillinsomestrat…     

Coding of odor intensity in a steady-state deterministic model of an olfactory receptor neuron

The coding of odor intensity by an olfactory receptor neuron model was studied under steady-state stimulation. Our model neuron is an elongated cylinder consisting of the following three components: a sensory dendritic region bearing odorant receptors, a passive region consisting of proximal dendrite and cell body, and an axon. First, analytical solutions are given for the three main physiological responses: (1) odorant-dependent conductance change at the sensory dendrite based on the Michaelis-Menten model, (2) generation and spreading of the receptor potential based on a new solution of the cable equation, and (3) firing frequency based on a Lapicque model. Second, the magnitudes of these responses are analyzed as a function of odorant concentration. Their dependence on chemical, electrical, and geometrical parameters is examined. The only evident gain in magnitude results from the activation-to-conductance conversion. An optimal encoder neuron is presented that suggests that increasing the length of the sensory dendrite beyond about 0.3 space constant does not increase the magnitude of the receptor potential. Third, the sensivities of the responses are examined as functions of (1) the concentration at half-maximum response, (2) the lower and upper concentrations actually discriminated, and (3) the width of the dynamic range. The overall gain in sensitivity results entirely from the conductance-to-voltage conversion. The maximum conductance at the sensory dendrite appears to be the main tuning constant of the neuron because it determines the shift toward low concentrations and the increase in dynamic range. The dynamic range of the model cannot exceed 5.7 log units, for a sensitivity increase at low odor concentration is compensated by a sensitivity decrease at high odor concentration.