Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences

To study the evolutionary relationships among the four living gymnosperm orders and the interfamilial relationships in each order, a set of 65 nuclear 18S rRNA sequences from ferns, gymnosperms, and angiosperms was analyzed using the neighbor-joining and maximum-parsimony methods. With Selaginella as the outgroup, the analysis strongly indicates that the seed plants form a monophyletic group with the ferns as a sister group. Within the seed plants the angiosperms are clearly a monophyletic group. Although the bootstrap support for the monophyly of the gymnosperm clade is moderate, the monophyly is further supported by its lack of angiosperm-specific indels. Within the gymnosperms there appear to be three monophyletic clades: Cycadales-Ginkgoales, Gnetales, and Coniferales. The cycad-ginkgo clade is the earliest gymnosperm lineage. Given the strong support for the sister group relationship between Gnetales and Coniferales, it is unlikely that Gnetales is a sister group of the angiosperms, contrary to the view of many plant taxonomists. Within Coniferales, Pinaceae is monophyletic and basal to the remaining conifer families, among which there are three monophyletic clades: Phyllocladaceae-Podocarpaceae, Araucariaceae, and Sciadopityaceae-Taxaceae-Cephalotaxaceae-Taxodiacea e-Cupressaceae. Within the latter clade, Sciadopityaceae may be an outgroup to the other four families. Among the angiosperms, no significant cluster at the level of subclass was found, but there was evidence that Nymphaeaceae branched off first. Within the remaining angiosperms, the monocots included in this study are nested and form a monophyletic group. This study attests to the utility of nuclear 18S rRNA sequences in addressing relationships among living gymnosperms. Considerable variation in substitution rates was observed among the ferns and seed plants.     

Floral homeotic genes were recruited from homologous MADS-box genes preexisting in the common ancestor of ferns and seed plants

Flowers sensu lato are short, specialized axes bearing closely aggregated sporophylls. They are typical for seed plants (spermatophytes) and are prominent in flowering plants sensu stricto (angiosperms), where they often comprise an attractive perianth. There is evidence that spermatophytes evolved from gymnosperm-like plants with a fern-like mode of reproduction called progymnosperms. It seems plausible, therefore, that the stamens/carpels and pollen sacs/nucelli of spermatophytes are homologous to fern sporophylls and sporangia, respectively. However, the exact mode and molecular basis of early seed and flower evolution is not yet known. Comparing flower developmental control genes to their homologs from lower plants that do not flower may help to clarify the issue. We have isolated and characterized MADS-box genes expressed in gametophytes and sporophytes of the fern Ceratopteris. The data indicate that at least two different MADS-box genes homologous to floral homeotic genes existed in the last common ancestor of contemporary vascular plants, some descendants of which underwent multiple duplications and diversifications and were recruited into novel developmental networks during the evolution of floral organs.     

A common ancestor for oxygenic and anoxygenic photosynthetic systems: a comparison based on the structural model of photosystem I

High molecular mass fractions of lignin and humic compounds in sediments and waters downstream of a pulp mill were characterized applying pyrolysis-gas chromatography-mass spectrometry. The results were compared to those obtained using reversed phase HPLC on the cupric oxide oxidation products. The chromatographic data of both pyrolysis and cupric oxide oxidation were also subjected to the principal component analysis (PCA). The sediment samples and fractions obtained by ultrafiltration of river water samples were freeze dried prior to characterization. The sediment samples were also extracted using 2 M sodium hydroxide solution. The extracts were ultrafiltrated, freeze dried and compared to the freeze dried original sediments using the procedures mentioned above. The amounts of HMMs obtained from the sediments ranged from 62 mg to 97 mg per one gram of sediment. Gel permeation chromatography was applied to samples obtained from sediments by extraction with tetrahydrofuran. The weight average molecular weights of these fractions were in the range of 1500-2300 amu.     

Micronuclear and macronuclear sequences of a Euplotes crassus gene encoding a putative nuclear protein kinase

Tacrolimus (FK506) is a new immunosuppressive agent that has recently been given to recipients of liver transplants. Multicentre studies conducted in the United States and Europe have reported that tacrolimus is superior to cyclosporine in preventing allograft rejection. The absorption of tacrolimus is independent of bile, and, therefore, therapeutic blood levels are usually achieved by taking oral preparations within 72 hours of liver transplantation. Compared with the use of cyclosporine, this regimen has resulted in shorter hospital stays and reduced costs. Tacrolimus does not cause hirsutism or gingival hyperplasia, which are common disfiguring complications of cyclosporine. Serious neurological side effects, lymphoproliferative disorders and hypertrophic cardiomyopathy have recently been reported in children taking high doses of tacrolimus. When lower doses of tacrolimus are used in primary immunosuppressive therapy, the incidence of neurological side effects and lymphoproliferative disorders of tacrolimus and cyclosporine have been reported to be similar. Hence, tacrolimus is a potent immunosuppressant that has many advantages over cyclosporine but must be used cautiously, since high doses have been associated with an increased incidence of lymphoproliferative disorders and cardiomyopathy.     

Molecular reconstruction and homology modelling of the catalytic domain of the common ancestor of the haemostatic vitamin-K-dependent serine proteinases

The vitamin-K-dependent serine proteinases of coagulation have evolved by a process of gene duplication and divergence, acquiring along the way a considerable degree of functional diversity that has equipped them for their different roles in haemostasis. The cDNA sequences encoding the catalytic domains of the early mammalian ancestors of five vitamin-K-dependent factors (factors VII, IX and X, protein C and prothrombin) were reconstructed by employing cDNA sequence data from a range of extant mammals and by using established phylogenies. The cDNA sequence of the putative common ancestor of these early mammalian proteins was then reconstructed from the five sequences by using a deduced phylogeny that was different in a number of respects from those previously proposed. Factor IX is proposed to have branched off early on, followed by protein C and prothrombin and finally factors VII and X. Significant differences in mutation rates were observed between proteins within a species; factor IX exhibited a lower mutation rate than the other proteins, consistent with its early emergence. Differences in mutation rates were also observed between species for a given protein and these exhibited an inverse correlation with generation time. A biophysically plausible structure for the ancestral vitamin-K-dependent factor protein was constructed by comparative methods. Studies of the functional architecture of this model provide new insights into the evolution of protein-binding specificity in this family of proteins.     

A/T-rich sequences act as quantitative enhancers of gene expression in transgenic tobacco and potato plants

This study is the first to report approximations of energy requirements for male and female breast-fed and formula-fed infants based on individual estimates of total daily energy expenditure (TDEE) and energy deposition derived from total body fat (TBF) and fat-free mass (FFM) gain as determined by total-body electrical conductivity. In 46 healthy, full-term infants the effect of > or = 4 mo of exclusive breast-feeding compared with formula feeding on macronutrient and energy intake, TDEE, energy deposition, and growth were investigated prospectively. Metabolizable energy intake (MEI) was assessed from macronutrient intake by test weighing (MEI-TW) and from the sum of TDEE and energy deposition (MEI-Pred). At 1-2, 2-4, 4-8, and 8-12 mo of age MEI-Pred averaged 431 +/- 38, 393 +/- 33, 372 +/- 33, and 355 +/- 21 kJ x kg(-1) x d(-1) for boys, and 401 +/- 59, 376 +/- 25, 334 +/- 33, and 326 +/- 17 kJ x kg(-1) x d(-1) for girls. No significant difference between breast-fed and formula-fed infants was found with respect to weight, length, head circumference, TBF, FFM, and TDEE at all ages, or for gain in length, weight, TBF, and FFM. MEI-TW was significantly different between feeding groups at 1-4 mo of age (formula-fed being greater than breast-fed, P < 0.005). This feeding effect, however, was not significant for MEI-Pred (MJ/d). MEI-TW differed from MEI-Pred only in breast-fed infants at 1-4 mo (P < 0.05 at 2-4 mo). The data from this study indicate that energy requirements in infants are lower than the recommendations in guidelines currently in use.     

Epidemiologic findings on the relationship of time of day and time since last meal to glucose tolerance

Data from 10,559 men and women, age 30-64, participating in the morning and afternoon in a Chicago Health Department multiphasic screening project, were used to determine the effects of time of day and time since last meal on the values for plasma glucose one and two hours following oral challenge with 100 gm. of glucose. Mean plasma glucose values and rates of suspect glucose intolerance (based on several cutpoints) were sizeably higher in the afternoon than in the morning. In addition, plasma glucose values increased with time elapsed since the last meal, up to 10 hours postprandially. Thereafter, both one- and two-hour plasma glucose values tended to exhibit a decline. Analysis of covariance confirmed that fluctuations in glucose tolerance were related to time of day and time since last meal, but the effects of each parameter were exerted independently.     

Evidence for an essential non-Watson-Crick interaction between the first and last nucleotides of a nuclear pre-mRNA intron

Nuclear pre-messenger RNA splicing requires the action of five small nuclear (sn) RNAs, U1, U2, U4, U5 and U6, and more than 50 proteins. The mechanistic similarity of nuclear pre-mRNA splicing and group II self-splicing suggests that many of the central processes of nuclear pre-mRNA splicing are based on RNA-RNA interaction. To understand the mechanism of pre-mRNA splicing, the interactions, and their temporal relationships, that occur between the snRNAs and the pre-mRNA during splicing must be identified. Several snRNA-snRNA and snRNA-intron interactions have been demonstrated but the putative RNA-based interactions that recognize the AG dinucleotide at the 3' splice site during 3' cleavage and exon ligation are unknown. We report here the reciprocal suppression between 5' and 3' splice site mutations in the yeast actin intron, and propose that the 3' splice site is positioned for 3' cleavage and exon ligation, at least in part, through a non-Watson-Crick interaction between the guanosines at the 5' and 3' splice sites.     

Allele-specific late replication and fragility of the most active common fragile site, FRA3B

FRA3B at 3p14.2 is the most active of the common fragile sites in the human genome and is expressed when cells are exposed to the DNA replication inhibitor, aphidicolin. Several lines of evidence suggest that fragile sites are regions of late replication. To elucidate the relationship between the timing of replication across the FRA3B region and its corresponding fragility, we labeled cells with 5-bromo-2'-deoxyuridine (BrdU) and adopted an immunofluorescent procedure to visualize late replicating DNA (BrdU-substituted DNA) in metaphase chromosomes. We also chose 21 markers along the FRA3B region and analyzed the timing of replication using BrdU-labeled DNA from different stages of the cell cycle sorted by flow cytometry. Our results show that there are two distinct alleles that replicate at different stages in the cell cycle and that breaks/gaps preferentially occurred on the chromosome 3 with the late replication allele. These results provide direct evidence that allele-specific late replication is involved in the fragility of the most active common fragile site, FRA3B.     

Endocytosis of the common cytokine receptor gammac chain. Identification of sequences involved in internalization and degradation

The common cytokine receptor gammac, shared by interleukin 2, 4, 7, 9, and 15 receptors, has a major role in lymphocyte proliferation and differentiation, leading, when mutated, to a genetic disease, X-linked severe combined immunodeficiency. In this study, we report that gammac is internalized and degraded in lymphoid cells. To identify gammac regions involved in sorting along the endocytic pathway, we have studied a chimeric protein composed of the extracellular part of interleukin 2-receptor alpha and transmembrane and intracellular part of gammac, alpha gamma gammawt. When transfected in Jurkat T cells, alpha gamma gammawt is as efficiently internalized and degraded as gammac, demonstrating that the transmembrane and cytosolic tail of gammac carry sequences involved in this process. To identify these motifs, we have analyzed the trafficking of chimeric proteins with serial truncations in their cytosolic tail. Internalization studies showed that the cytosolic tail of gammac contains three regions located between cytosolic amino acids 1-35, 35-40, and 40-65 involved in gammac endocytosis. Successive deletions of these motifs result in reduced endocytosis. One region containing the 5 cytosolic amino acids 36-40 is essential to direct gammac to the degradation pathway. These sorting sequences, by participating in the fine tuning of cell surface gammac expression, might somewhat regulate the cell responsiveness to interleukins whose receptors share this component.     

Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria

Negative pressure transients (NPT) recorded in a single closing event of mechanical valves in the mitral position in an in vitro setup are compared with data recorded in the left atrium in vivo with the valves implanted in the mitral position in an animal model. The loading at valve closure (dP/dtCL) computed from the in vivo ventricular pressure recording (ranging from 700 to 2300 mm Hg/s) agreed with the magnitudes predicted in our earlier in vitro experiments (750-3000 mm Hg/s). The NPT signals and the corresponding power spectral density plots from the in vivo data were in qualitative agreement with those recorded in vitro. The NPT magnitudes were found to be below the vapor pressure for blood in mechanical valves with rigid occluders suggesting a potential for the valve to cavitate in vivo. Our in vivo results also suggest that the valves with flexible occluders are less likely to cavitate. The correlation of the in vitro and in vivo data also suggests that the flexibility of valve housing used in the in vitro studies is not an important factor in the dynamics of mechanical valve closure in vivo.     

Identification of functional elements in the promoter region of the human gene for thymidylate synthase and nuclear factors that regulate the expression of the gene

To identify the essential motifs of the promoter of the human gene for thymidylate synthase (TS), we constructed a set of deletion mutants from the 5'-terminal region of the human TS gene. From the results of assays of the expression of chloramphenicol acetyltransferase (CAT), we identified two functional elements with positive effects on the promoter activity: a CACCC box (CCACACCC) and an Sp1-binding motif (GAGGCGGA) that was homologous to the Sp1-binding site in the mouse TS gene. In addition, negative regulatory sequences were identified between the two positive elements and in the region upstream of the CACCC box. The results of gel mobility shift analyses suggested that Sp1 binds to the Sp1-binding motif of the human TS gene promoter and that multiple nuclear factors that are related to Sp1 bind to the CACCC box. Furthermore, the binding of Sp1 to mutated Sp1-binding motifs in the promoter region of the human TS gene was correlated with the promoter activity, as measured by the CAT assay. Therefore, the Sp1 motif seems to be a major contributor to the basic promoter activity of the human TS gene, although multiple positive and negative regulatory elements are involved in the regulated expression of this gene.