Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project

BLASTX alignment between 189.5 Mb of rice genomic sequence and translated Arabidopsis thaliana annotated coding sequences (CDS) identified 60 syntenic regions involving 4–22 rice orthologs covering ≤3.2 cM (centiMorgan). Most regions are <3 cM in length. A detailed and updated version of a table representing these regions is available on our web site. Thirty-five rice loci match two distinct A.thaliana loci, as expected from the duplicated nature of the A.thaliana genome. One A.thaliana locus matches two distinct rice regions, suggesting that rice chromosomal sequence duplications exist. A high level of rearrangement characterizing the 60 syntenic regions illustrates the ancient nature of the speciation between A.thaliana and rice. The apparent reduced level of microcollinearity implies the dispersion to new genomic locations, via transposon activity, of single or small clusters of genes in the rice genome, which represents a significant additional effector of plant genome evolution.     

Effects of matriconditioning on onion seed germination, seedling emergence and associated physical and metabolic events

The effect of matriconditioning, the physiological presowing seed technique, using Micro-Cel E on Allium cepa L. cv. Czerniakowska seed quality was studied. Several ratios of seeds, carrier, water and time of priming were tested. The most effective treatment for improving onion seed germination at most tested temperatures was priming to a ratio of 2 g seed:1 g Micro-Cel:3 g water for 5 days in light at 15 °C. Matriconditioning greatly improved the germination and emergence percentage, seedling fresh and dry weight and reduced electrolyte leakage compared to that of untreated seeds; this beneficial effect was especially evident at suboptimal temperatures. Matriconditioning improved the germinability of aged seeds, the effect being more pronounced in the more aged seeds. No significant differences in ethylene production by primed and non-primed seeds were observed in the absence of its precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), but its presence during imbibition caused an increase in ethylene production; an enhanced activity of in vivo ACC oxidase in Allium cepa matriconditioned seeds in comparison to untreated seeds, indicates that the endogenous level of ACC is a limiting factor of ethylene production. Likewise, the activity of ACC oxidase isolated from matriconditioned seeds was higher than that from untreated seeds. Higher endo--mannanase and total dehydrogenase activities were observed in primed air-dried seeds in comparing to non-primed seeds.     

A potential mechanism for the impairment of nitric oxide formation caused by prolonged oral exposure to arsenate in rabbits

We have recently found evidence for impairment of nitric oxide (NO) formation and induction of oxidative stress in residents of an endemic area of chronic arsenic poisoning in Inner Mongolia, China. To investigate the underlying mechanisms responsible for these phenomena, a subchronic animal experiment was conducted using male New Zealand White rabbits. After 18 weeks of continuous exposure of rabbits to 5 mg/l of arsenate in drinking water, a significant decrease in systemic NO production occurred, as shown by significantly reduced plasma NO metabolites levels (76% of control) and a tendency towards decreased serum cGMP levels (81.4% of control). On the other hand, increased oxidative stress, as shown by significantly increased urinary hydrogen peroxide (H(2)O(2)) (120% of control), was observed in arsenate-exposed rabbits. In additional experiments measuring aortic tension, the addition of either the calcium ionophore A23187 or acethylcholine (ACh) induced a transient vasoconstriction of aortic rings prepared from arsenate-exposed rabbits, but not in those prepared from control animals. This calcium-dependent contractility action observed in aorta rings from arsenate-exposed rabbits was markedly attenuated by the superoxide (O2(.-)) scavenging enzyme Cu, Zn-SOD, as well as diphenyleneiodonium (DPI) or N(G)-nitro-L-arginine methyl ester (L-NAME), which are inhibitors for nitric oxide synthase (NOS). However, the cyclooxygenase inhibitor indomethacin or the xanthine oxidase blocker allopurinol had no effect on this vasoconstriction. These results suggest that arsenate-mediated reduction of systemic NO may be associated with the enzymatic uncoupling reaction of NOS with a subsequent enhancement of reactive oxygen species such as O2(.-), an endothelium-derived vasoconstricting factor. Furthermore, hepatic levels of (6R)-5,6,7,8-tetrahydro-L-biopterin (BH(4)), a cofactor for NOS, were markedly reduced in arsenate-exposed rabbits to 62% of control, while no significant change occurred in cardiac L-arginine levels. These results suggest that prolonged exposure of rabbits to oral arsenate may impair the bioavailability of BH(4) in endothelial cells and, as a consequence, disrupt the balance between NO and O2(.-) produced from endothelial NOS, such that enhanced free radicals are produced at the expense of NO.     

Cytotoxic activity of flavonoids and extracts from Retama sphaerocarpa Boissier

Seven flavonoids isolated from chloroform, ethyl acetate and butanol extracts, obtained from the aerial parts of Retama sphaerocarpa, have been assessed for cytotoxic activity against three human cancer cell lines: TK-10 (renal adenocarcinoma), MCF-7 (breast adenocarcinoma) and UACC-62 (melanoma), using the SRB assay. All of them, extracts and flavonoids, were actives in, at least, one of the three cell lines at the recommended National Cancer Institute doses. They produce a dose-dependent inhibition of cell growth at concentrations in the 10(-6)-10(-4) M and 25-250 microg/ml range for the flavonoids and extracts respectively, being the flavonol rhamnazin the most cytotoxic.     

Cation Permeability and Selectivity of a Root Plasma Membrane Calcium Channel

Calcium channels in the plasma membrane of root cells fulfill both nutritional and signaling roles. The permeability of these channels to different cations determines the magnitude of their cation conductances, their effects on cell membrane potential and their contribution to cation toxicities. The selectivity of the rca channel, a Ca²⁺-permeable channel from the plasma membrane of wheat (Triticum aestivum L.) roots, was studied following its incorporation into planar lipid bilayers. The permeation of K⁺, Na⁺, Ca²⁺ and Mg²⁺ through the pore of the rca channel was modeled. It was assumed that cations permeated in single file through a pore with three energy barriers and two ion-binding sites. Differences in permeation between divalent and monovalent cations were attributed largely to the affinity of the ion binding sites. The model suggested that significant negative surface charge was present in the vestibules to the pore and that the pore could accommodate two cations simultaneously, which repelled each other strongly. The pore structure of the rca channel appeared to differ from that of L-type calcium channels from animal cell membranes since its ion binding sites had a lower affinity for divalent cations. The model adequately accounted for the diverse permeation phenomena observed for the rca channel. It described the apparent submillimolar K _m for the relationship between unitary conductance and Ca²⁺ activity, the differences in selectivity sequences obtained from measurements of conductance and permeability ratios, the changes in relative cation permeabilities with solution ionic composition, and the complex effects of Ca²⁺ on K⁺ and Na⁺ currents through the channel. Having established the adequacy of the model, it was used to predict the unitary currents that would be observed under the ionic conditions employed in patch-clamp experiments and to demonstrate the high selectivity of the rca channel for Ca²⁺ influx under physiological conditions. Received: 23 August 1999/Revised: 12 November 1999     

The mitochondrial DNA of <Emphasis Type="Italic">Dictyostelium discoideum</Emphasis>: complete sequence,gene content and genome organization

We present an overview of the gene content and organization of the mitochondrial genome of Dictyostelium discoideum. The mitochondria genome consists of 55,564?bp with an A + T content of 72.6%. The identified genes include those for two ribosomal RNAs (rnl and rns), 18 tRNAs, ten subunits of the NADH dehydrogenase complex (nad1, 2, 3, 4, 4L, 5, 6, 7, 9 and 11), apocytochrome b (cytb), three subunits of the cytochrome oxidase (cox1/2 and 3), four subunits of the ATP synthase complex (atp1, 6, 8 and 9), 15 ribosomal proteins, and five other ORFs, excluding intronic ORFs. Notable features of D. discoideum mtDNA include the following. (1) All genes are encoded on the same strand of the DNA and a universal genetic code is used. (2) The cox1 gene has no termination codon and is fused to the downstream cox2 gene. The 13 genes for ribosomal proteins and four ORF genes form a cluster 15.4?kb long with several gene overlaps. (3) The number of tRNAs encoded in the genome is not sufficient to support the synthesis of mitochondrial protein. (4) In total, five group I introns reside in rnl and cox1/2, and three of those in cox1/2 contain four free-standing ORFs. We compare the genome to other sequenced mitochondrial genomes, particularly that of Acanthamoeba castellanii.     

Role of glycosphingolipid microdomains in CD4-dependent HIV-1 fusion

The fusion of HIV-1 with the plasma membrane of CD4+ cells is triggered by the interaction of HIV-1 surface envelope glycoprotein gp120 with the CD4 receptor, and requires coreceptors (CCR5 and CXCR4). Recent advances in the study of HIV-1 entry into CD4+ cells suggest that glycosphingolipids (GSL) may also participate in the fusion process. GSL are organized in functional microdomains which are associated with specific membrane proteins such as CD4. GSL-enriched microdomains were purified from human lymphocytes and reconstituted as a monomolecular film at the air-water interface of a Langmuir film balance. Surface pressure measurements allowed to characterize the sequential interaction of GSL with CD4 and with gp120. Using this approach, we identified globotriaosylceramide (Gb3) and ganglioside GM3 as the main lymphocyte GSL recognized by gp120. In both cases, the interaction was saturable and dramatically increased by CD4. We propose that GSL microdomains behave as moving platforms allowing the recruitment of HIV-1 coreceptors after the initial interaction between the viral particle and CD4. According to this model, the GSL microdomain may: i) stabilize the attachment of the virus with the cell surface through multiple low affinity interactions between the V3 domain of gp120 and the carbohydrate moiety of GSL, and ii) convey the virus to an appropriate coreceptor by moving freely in the outer leaflet of the plasma membrane. This model can be extrapolated to all envelope viruses (e.g. influenza virus) that use cell surface GSL of the host cells as receptors or coreceptors.     

Comparative cytogenetics of hamsters of the genus Calomyscus

Karyotypes of Calomyscus from different regions of Turkmenistan, Iran, and Azerbaijan were studied using chromosome banding (G- and C-banding) and analyses of meiosis in laboratory hybrids. Extensive variation in the diploid number and the number of autosomal arms (FNa) was revealed (2n = 30, FNa = 44; 2n = 32, FNa = 42; 2n = 44, FNa = 46; 2n = 44, FNa = 58; 2n = 37, FNa = 44; 2n = 50, FNa = 50; 2n = 52, FNa = 56). Centric and tandem fusions and heterochromatin changes were identified as the major modes of karyotype evolution in this group. Natural hybrids between individuals with different karyotypes were recorded, and regular chromosome pairing in meiosis was observed in laboratory hybrids. Fluorescence in situ hybridization with a 353-bp BspRI complex tandem repeat indicated that chromosomal repatterning occurred recently within the genus. There is no unequivocal evidence suggesting the role of chromosomal change in the speciation of the populations of Calomyscus examined.