Geminiviruses: a tale of a plasmid becoming a virus

Background  

Geminiviruses (family Geminiviridae) are small single-stranded (ss) DNA viruses infecting plants. Their virion morphology is unique in the known viral world – two incomplete T = 1 icosahedra are joined together to form twinned particles. Geminiviruses utilize a rolling-circle mode to replicate their genomes. A limited sequence similarity between the three conserved motifs of the rolling-circle replication initiation proteins (RCR Reps) of geminiviruses and plasmids of Gram-positive bacteria allowed Koonin and Ilyina to propose that geminiviruses descend from bacterial replicons.     

Characterization of a new strain of a purple nonsulfur bacterium from a thermal spring

A new budding purple nonsulfur bacterium of the genus Rhodobacter (strain Ku-2) was isolated from a mat of a moderately thermal spring (Baikal rift zone, Buryatia, Russia). The bacterium had lamellar photosynthetic membranes, which are typical of only one Rhodobacter species, Rba. blasticus. The cells contained spheroidene carotenoids and bacteriochlorophyll a (Bchl a). In vivo absorption spectrum of the cells, with the major maximum at 863 nm and an additional peak at 887 nm, is characteristic of the pigment-protein complexes of Bchl a-containing membranes. The previously described Rba. blasticus strains do not exhibit the 887-nm maximum. The new isolate was photoheterotrophic, with optimal growth occurring at 35°C, 3 g/L NaCl, and pH 7–8. The DNA G+C content was 64.4 mol %. The similarity between the 16S rRNA gene sequences of strain Ku-2 and the Rba. blasticus type strain was 98.7%. The PufM amino acid sequences of strain Ku-2 and the earlier studied Rba. blasticus type strain were 89.5 % identical. Thus, strain Ku-2 belongs to the genus Rhodobacter and is phylogenetically close to Rba. blasticus.     

Transformation of a psychrotrophic bacterium with a plasmid from a mesophile

The psychrotrophic bacteriumBacillus psychrophilus was transformed with the broadhost-range plasmid pC194. The ability of the transformant to express chloramphenicol (CAM) resistance and the possible effects of such expression on the physiology of the psychrotroph were examined. The transformant exhibited growth rates, filament formation at elevated temperatures, synthesis of cold shock proteins and cold acclimation proteins, similar to the parentalB. psychrophilus.     

Effects of a disease affecting a predator on the dynamics of a predator-prey system

We study the effects of a disease affecting a predator on the dynamics of a predator-prey system. We couple an SIRS model applied to the predator population, to a Lotka-Volterra model. The SIRS model describes the spread of the disease in a predator population subdivided into susceptible, infected and removed individuals. The Lotka-Volterra model describes the predator-prey interactions. We consider two time scales, a fast one for the disease and a comparatively slow one for predator-prey interactions and for predator mortality. We use the classical “aggregation method” in order to obtain a reduced equivalent model. We show that there are two possible asymptotic behaviors: either the predator population dies out and the prey tends to its carrying capacity, or the predator and prey coexist. In this latter case, the predator population tends either to a “disease-free” or to a “disease-endemic” state. Moreover, the total predator density in the disease-endemic state is greater than the predator density in the “disease-free” equilibrium (DFE).     

Application of a novel method for age estimation of a baleen whale and a porpoise

Eyeballs from 121 fin whales (Balaenoptera physalus) and 83 harbor porpoises (Phocoena phocoena) were used for age estimation using the aspartic acid racemization (AAR) technique. The racemization rate (k_Asp) for fin whales was established from 15 fetuses (age 0) and 15 adult whales where age was estimated by reading growth layer groups (GLGs) in the earplugs. The (k_Asp) for harbor porpoises was derived from 15 porpoises (two calves and 13 > 1 yr old) age‐estimated by counting GLGs in the teeth and two calves classified to age based on length. The (k_Asp) values were estimated by regression of GLGs against D/L ratios. For the fin whales an (k_Asp) of 1.15 × 10^?3/yr (SE ± 0.00005) and a D/L ratio at birth [(D/L)₀] of 0.028 (SE ± 0.0012) were estimated, which is in agreement with rates for other mysticeti. For the harbor porpoises a (k_Asp) of 3.10 × 10^?3/yr (SE ± 0.0004) and a (D/L)₀ value of 0.023 (SE ± 0.0018) were estimated, which is considerably higher than found for other cetaceans. Correlation between chosen age estimates from AAR and GLG counts indicated that AAR might be an alternative method for estimating age in marine mammals.     

The dynamics of a model of a plankton-nutrient interaction

A stability analysis is given for a model of plankton dynamics introduced by Wroblewskiet al. (Global Biogeochem. Cycles 2, 199–218, 1988). The detailed dependence of the steady-states and their stability on the various model parameters is explicitly presented and analysed. It is shown that under certain conditions the coexistence of phytoplankton and zooplankton occurs in an orbitally stable oscillatory mode. A distinguished parameter is varied and the steady-states computed. The significance of the lack of stable steady-states leading to periodic population levels is investigated and related to certain oceanographic data. Partially supported by NSF Grant DMS-8902712. Supported by New Zealand University Grants Committee Postdoctoral Fellowship.     

Recognition of a Flipped Base in a Hairpinloop DNA by a Small Peptide

Two tiny hairpin DNAs, CORE (dAGGCTTCGGCCT) and AP2 (dAGGCTXCGGCCT; X: abasic nucleotide), fold into almost the same tetraloop hairpin structure with one exception, that is, the sixth thymine (T6) of CORE is exposed to the solvent water (Kawakami, J. et al., Chem. Lett. 2001, 258–259). In the present study, we selected small peptides that bind to CORE or AP2 from a combinatorial pentapeptide library with 2.5 × 10⁶ variants. On the basis of the structural information, the selected peptide sequences should indicate the essential qualifications for recognition of the hairpin loop DNA with and without a flipped base. In the selected DNA binding peptides, aromatic amino acids such as histidine for CORE and glutamine/aspartic acid for AP2 were found to be abundant amino acids. This amino acid preference suggests that CORE-binding peptides use π–π stacking to recognize the target while hydrogen bonding is dominant for AP2-binding peptides. To investigate the binding properties of the selected peptide to the target, surface plasmon resonance was used. The binding constant of the interaction between CORE and a CORE-binding peptide (HWHHE) was about 1.1 × 10⁶ M^?1 at 25°C and the resulting binding free energy change at 25°C (ΔG°₂₅) was ?8.2 kcal mol^?1. The binding of the peptide to AP2 was also analyzed and the resulting binding constant and ΔG°₂₅ were about 4.2 × 10⁴ M^?1 and ?6.3 kcal mol^?1, respectively. The difference in the binding free energy changes (ΔΔG°₂₅) of 1.9 kcal mol^?1 was comparable to the values reported in other systems and was considered a consequence of the loss of π–π stacking. Moreover, the stabilization effect by stacking affected the dissociation step as well as the association step. Our results suggest that the existence of an aromatic ring (T6 base) produces new dominant interactions between peptides and nucleic acids, although hydrogen bonding is the preferable mode of interaction in the absence of the flipping base. These findings regarding CORE and AP2 recognition are expected to give useful information in the design of novel artificial DNA binding peptides.     

Identification of miRNAs in a Liver of a Human Fetus by a Modified Method

Background

miRNAs are 17–25 nucleotides long RNA molecules that have been found to regulate gene expression in human cells. There are studies showing that different groups of miRNAs are involved in development of different tissues. In hepatocytes there are reported particular types of miRNAs that regulate gene expression.

Methods

We established a human fetal liver cDNA library by a modified cloning protocol. Then plasmid isolation from the colonies was performed. After sequencing and database searching, the miRNAs were recognized. RT-PCR and sequencing were carried out to validate the miRNAs detected. Real-time PCR was used to analyze the expression of each miRNA.

Results

One novel miRNA was discovered, together with another 35 previously-known miRNAs in the fetal liver. Some of them existed in variants. The miRNAs identified were validated by RT-PCR and sequencing. Quantitative analysis showed that they have variable expression.

Conclusion

Our results indicate that a special group of miRNAs may play an important role in fetal liver development in a synergistic manner.     

Living inside a sponge skeleton: the association of a sponge,a macroalga and a diatom

The relationships between sponges and macroalgae have been poorly investigated, especially in temperate waters. This work describes the consortium between the dictyoceratid sponge Dysidea pallescens and the red alga Acrochaetium spongicola permeating spongin fibres in the Mediterranean Sea; moreover, this is the first report of a diatom, Amphora pediculus, living also inside the spongin skeleton. The annual trend of the total algal biomass did not vary over time in relation to the temperature, irradiance and incorporation of foreign bodies. Our analyses, conducted by light and electron microscopy, suggest that both the macroalga and the diatom invade the skeleton of the sponge from the external environment, and that the benthic diatom, epiphyte of the macroalga, is passively carried inside the fibres through the growth of Acrochaetium spongicola. All the examined samples of D. pallescens showed that the macroalga permeated at least some fibres, while the presence of the diatom was occasional. The superficial layer of the sponge, thin and reticulate, likely allows the passage of the light and ensures the algal survival inside the sponge tissue. The high occurrence of the association with A. spongicola, together with the morphological adaptations of the sponge favouring the algal life, suggest that the relationship is mutualistic. The possible benefits for the involved partners are hypothesized. The taxonomy and ecology of endozoic Acrochaetiales are controversial due to the reduced size of thalli, the absence of peculiar diagnostic characters and unknown reproductive structures. Therefore, detailed studies on the relationships between the algae and their hosts will provide helpful information for the algal identification.     

Isolation of a complementing activity for a dna-B mutant

A cell free extract which displays temperature sensitive DNA synthesis in the presence of single strand DNA and ATP was prepared from a $\text{dna-B}$ mutant. Following an activity which would reverse this temperature sensitivity, a protein fraction was isolated. The absence of this fraction in a $\text{dna-B}$ mutant indicates that this protein corresponds to the $\text{Dna-B}$ product.     

High-resolution structure of a self-assembly-competent form of a hydrophobic peptide captured in a soluble beta-sheet scaffold

β-Rich self-assembly is a major structural class of polypeptides, but still little is known about its atomic structures and biophysical properties. Major impediments for structural and biophysical studies of peptide self-assemblies include their insolubility and heterogeneous composition. We have developed a model system, termed peptide self-assembly mimic (PSAM), based on the single-layer β-sheet of Borrelia outer surface protein A. PSAM allows for the capture of a defined number of self-assembly-like peptide repeats within a water-soluble protein, making structural and energetic studies possible. In this work, we extend our PSAM approach to a highly hydrophobic peptide sequence. We show that a penta-Ile peptide (Ile₅), which is insoluble and forms β-rich self-assemblies in aqueous solution, can be captured within the PSAM scaffold in a form capable of self-assembly. The 1.1-Å crystal structure revealed that the Ile₅ stretch forms a highly regular β-strand within this flat β-sheet. Self-assembly models built with multiple copies of the crystal structure of the Ile₅ peptide segment showed no steric conflict, indicating that this conformation represents an assembly-competent form. The PSAM retained high conformational stability, suggesting that the flat β-strand of the Ile₅ stretch primed for self-assembly is a low-energy conformation of the Ile₅ stretch and rationalizing its high propensity for self-assembly. The ability of the PSAM to “solubilize” an otherwise insoluble peptide stretch suggests the potential of the PSAM approach to the characterization of self-assembling peptides.     

Metabolism of a DDT metabolite via a chloroepoxide

The 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) metabolic intermediate 1-chloro-2,2-bis(p-chlorophenyl)ethene (DDMU) is partially metabolized in vivo by mice to 2-hydroxy-2,2-bis(p-chlorophenyl)acetic acid (αOH-DDA) and other metabolites which are excreted in urine. The subsequent DDT metabolic intermediates 1-chloro-2,2-bis(p-chlorophenyl)ethane (DDMS) and 1,1-bis(p-chlorophenyl)ethene (DDNU) are metabolized to αOH-DDA to a much lesser extent. These results imply that DDMU may be metabolized via an α-chloroepoxide. The authentic DDMU-epoxide, which after oral administration is excreted as αOH-DDA, is mutagenic in the Ames assay, and thermally rearranges rapidly to the corresponding α-chloroaldehyde, 2,2-bis(p-chlorophenyl)-2-chloroacetaldehyde (αCl-DDCHO). As expected αCl-DDCHO yielded the same urinary metabolites as DDMU-epoxide. This suggested metabolic pathway for DDMU via a chloroepoxide intermediate may account for the tumorigenicity of DDT in mice.     

Glycan expression as a tool for a deeper understanding of a reproductive gland in a skate of economic importance

Atlantoraja platana is an oviparous skate endemic to the south-west Atlantic Ocean, and is one of the skate species most exploited by local industrial bottom trawl fisheries. Oviparous elasmobranchs encapsulate their eggs in complex egg cases produced by the oviductal gland (OG). This organ is exclusively present in these fishes and comprises four distinct zones: club, baffle, papillary and terminal. The relative size and structural complexity of these zones correlate with mode of reproduction. Glycans are known to play major roles in reproduction so their distribution in each zone of the OG could explain the functional multiplicity of the gland in skates, but this topic has not been previously investigated. In this study, morphological, histochemical and lectin-histochemical analysis revealed various novel aspects of A. platana's OG. The club, papillary and terminal zones positively stained for periodic acid Schiff's reagent (PAS) and Alcian Blue (AB), indicating the presence of neutral and acid mucopolysaccharides. However, the buffle zone was negative for PAS and AB stains, but was positive for all the lectins used. Each zone of the OG had a characteristic pattern of glycan expression. Finally, we confirmed the presence of sperm but not sperm storage. This is the first lectin-histochemical study of the OG in chondrichtyan fish and it has proven to be an important tool to understand some of the mechanisms of fertility and reproductive success in economic important species such as A. platana.     

Measurement of the adhesion of a desmid to a substrate

The paper describes a hydrodynamic method by which the adhesive strength of the mucilage produced from the apical proes of Closterium acerosum has been measured. An equation used to determine the drag force on the cells is presented, as are some measured adhesive strengths of the Closterium mucus to glass slides.     

Order Parameters of a Transmembrane Helix in a Fluid Bilayer: Case Study of a WALP Peptide

A new solid-state NMR-based strategy is established for the precise and efficient analysis of orientation and dynamics of transmembrane peptides in fluid bilayers. For this purpose, several dynamically averaged anisotropic constraints, including ¹³C and ¹⁵N chemical shift anisotropies and ¹³C-¹⁵N dipolar couplings, were determined from two different triple-isotope-labeled WALP23 peptides (²H, ¹³C, and ¹⁵N) and combined with previously published quadrupolar splittings of the same peptide. Chemical shift anisotropy tensor orientations were determined with quantum chemistry. The complete set of experimental constraints was analyzed using a generalized, four-parameter dynamic model of the peptide motion, including tilt and rotation angle and two associated order parameters. A tilt angle of 21° was determined for WALP23 in dimyristoylphosphatidylcholine, which is much larger than the tilt angle of 5.5° previously determined from ²H NMR experiments. This approach provided a realistic value for the tilt angle of WALP23 peptide in the presence of hydrophobic mismatch, and can be applied to any transmembrane helical peptide. The influence of the experimental data set on the solution space is discussed, as are potential sources of error.     

Production of a fish taxocene in a Texas pond

Synopsis Production rates of seven species of fishes were determined for one year in a 0.95 ha pond. Total annual production of all fishes in the pond was 209 g m^–2y^–1 (after the subtraction of 16.2 g m^–2y^–1 of negative production). Over 90% of the production occurred in the months of June through September, with young-of-the-year fishes contributing 84% of the total. When Y of Y fishes shifted to benthic diets in the spring, the small biomass of benthos available could not sustain the large biomas of fish. Severe competition for the available food then resulted in decreased production rates for the entire fish taxocene.     

Carotenoids in floral parts of a narcissus, a daffodil and a tulip

1. The qualitative and quantitative distribution of carotenoids of the floral parts of three monocotyledons, the narcissus Scarlet Elegance, the daffodil King Alfred and the tulip Golden Harvest, were studied. β-Carotene, lutein or epoxy-β-carotenes were usually the main pigments, depending on the floral part and on the flower. When β-carotene was the major pigment there were only small amounts of, or sometimes no, epoxycarotenes. 2. Anthers, stigmas and styles of the three flowers did not possess any specific carotenoids but in some cases contained appreciable amounts of epoxycarotenoids. The possibility that these take part in reproduction is discussed. 3. The generalization that yellow flowers contained large amounts of xanthophylls and only traces of carotenes, whereas deep-orange flowers seemed to be characterized by the presence of large amounts of one carotene, was not always the correct one. It is suggested that the floral parts are yellow or orange depending on what carotenoids are present, which is the major one and the amount of total carotenoids, and also on the presence of other non-carotenoid pigments. 4. Two new probable isomers of 5,6:5′,6′-diepoxy-β-carotene were isolated and found together in various floral parts of the tulip Golden Harvest.     

Direct Calculation of a Tree Length Using a Distance Matrix

Comparative studies of tree-building methods have shown minimum evolution to be in general an accurate criterion for selecting a true tree. To improve the use of this criterion, this paper proposes a method for rapidly and directly calculating a length of a dichotomous tree without having to resort to branch length calculations. This direct calculation (DC) method applies to the complete final topology, giving equal importance to each branch after a dichotomy. According to this method, the tree length S _DC is S _DC =∑ _i ∑ _j (D _ij /2 ^Bij ) = (∑ _i<j ∑D _ij 2 ^Bmax−Bij )/2 ^{Bmax −1} where D _ij is the observed distance between taxa i and j, B _ij is the number of branches connecting i and j, Bmax is the greatest B _ij in the tree, and the powers of two are due to the dichotomy of the tree. This tree length expression may be used as a rapid method for selecting the shortest tree from a set of hypothetical or subobtimal trees. Received: 2 March 2000 / Accepted: 24 March 2000     

Computational design of a substrate specificity mutant of a protein

The wild-type trp repressor of E. coli bound 5-methoxytryptophan, a Trp analogue, less tightly than Trp. A mutant repressor (Val⁵⁸→Ala) that should bind 5-methoxytryptophan preferentially to Trp was computationally designed by free-energy calculations accompanied by free-energy decomposition. The designed mutant was demonstrated by experiments to bind 5-methoxytryptophan more tightly than Trp, consistent with the computational prediction. This success indicates the usefulness of free energy decomposition in protein design. Proteins 26:459–464 © 1996 Wiley-Liss, Inc.