Summary
We report on a genomic and functional analysis of a novel marine siphovirus, the Vibrio phage SIO‐2. This phage is lytic for related Vibrio species of great ecological interest including the ...broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V. harveyi ATTC BAA‐1116 and V. campbellii ATCC 25920). Vibrio phage SIO‐2 has a circularly permuted genome of 80 598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO‐2 capsid, which assembles as a large (80 nm) shell with a novel T = 12 symmetry. These atypical structural features confer on SIO‐2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO‐2 emerges as a model of considerable interest in ecological and evolutionary studies.
N-terminal myristoylation plays a vital role in membrane targeting and signal transduction in plant responses to environmental stress. Although N-myristoyltransferase enzymatic function is conserved ...across plant, animal, and fungal kingdoms, exact substrate specificities vary, making it difficult to predict protein myristoylation accurately within specific taxonomic groups.
A new method for predicting N-terminal myristoylation sites specifically in plants has been developed and statistically tested for sensitivity, specificity, and robustness. Compared to previously available methods, the new model is both more sensitive in detecting known positives, and more selective in avoiding false positives. Scores of myristoylated and non-myristoylated proteins are more widely separated than with other methods, greatly reducing ambiguity and the number of sequences giving intermediate, uninformative results. The prediction model is available at http://plantsp.sdsc.edu/myrist.html.
Superior performance of the new model is due to the selection of a plant-specific training set, covering 266 unique sequence examples from 40 different species, the use of a probability-based hidden Markov model to obtain predictive scores, and a threshold cutoff value chosen to provide maximum positive-negative discrimination. The new model has been used to predict 589 plant proteins likely to contain N-terminal myristoylation signals, and to analyze the functional families in which these proteins occur.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Traditionally, performing myocardial contrast echocardiography with OPTISON required maximal bolus dosing. However, sustained and consistent opacification of the myocardium would be preferable for ...perfusion imaging.
Images of 5 anesthetized dogs and 6 human volunteers were obtained with a second harmonic ultrasound system during bolus administration of OPTISON and 2 infusion techniques. One infusion technique used diluted OPTISON, and the other used the buoyant properties of OPTISON microspheres by placing the contrast agent between an infusion source and the intravenous site in a vertically oriented extension line (ELT). Myocardial intensities and in vitro microsphere characteristics were analyzed to assess the consistency of microsphere delivery over time.
In addition to providing higher myocardial opacification intensity than diluted infusions, ELT infusions provided consistent microsphere concentration, phantom enhancement, and near-peak bolus-level myocardial opacification for 7 to 15 minutes. The myocardial intensity at 3 and 5 minutes in human subjects during ELT infusions (30 mL/h; 2.5 mL) was lower (220 arbitrary units au and 165 au, respectively) but not significantly different (P =.3 and.1, respectively) than the peak myocardial intensity (265 au) after bolus administration.
This new ELT infusion method provides an acceptable alternative to bolus administration of OPTISON for prolonged myocardial opacification.
Wheat germ agglutinin (WGA) binds to the entire surface of Strongylocentrotus purpuratus sperm, and inhibits the egg jelly-induced acrosome reaction. The binding was found to be species dependent and ...was completely inhibited by 5 mM N-acetyl-D-glucosamine. Blockage of the acrosome reaction by WGA was bypassed by a combination of the ionophores A23187 and monensin, although neither ionophore was effective individually. These experiments suggest that WGA blocks both Ca2+uptake and Na+/H+exchange in these sperm, which was confirmed by direct measurements of45Ca2+uptake and H+efflux. The target of WGA in S. purpuratus sperm appears to be a membrane glycoprotein of Mr=210,000. Treatment of this protein with neuraminidase or endo-β-N-acetylglucosaminidase F abolished WGA binding.
Optison® is an ultrasound contrast agent, consisting of gas‐filled microspheres surrounded by a solid shell of heat‐denatured human albumin. Size‐distribution measurements of these microspheres are a ...critical stability indicating factor, because loss of encapsulated gas eliminates ultrasound contrast activity. Composition of the encapsulated gas is also critical, because air‐filled microspheres do not persist nearly as long in vivo as microspheres filled with less soluble gases. Optison® stability has been tested during exposure to chemical substances expected to dissolve microsphere shells. In addition, size‐distribution and gas‐composition measurements were used to evaluate the effects of external gas composition, elevated temperature, mixing, needle shear and pressure on product stability. Optison® microsphere shells dissolve only when exposed to relatively extreme chemical conditions, such as low pH (<4.0), detergents or chaotropic salts. The shells are highly gas‐permeable, and microspheres lose encapsulated gas rapidly and irreversibly when exposed to gas‐deficient liquids. Pressure, impact stress, and the application of ultrasound energy all cause liquids to become gas‐deficient, and also cause irreversible gas loss. Pressure sensitivity differs dramatically between mixed and unmixed microspheres, further supporting the conclusion that gas diffusion is the major cause of Optison® instability. To preserve the efficacy of Optison® as an ultrasound contrast agent, it is necessary to devote special attention to minimizing opportunities for gas exchange, mixing and exposure to gas‐deficient liquids, so that the size distribution and gas composition of the original product are maintained during handling.
Two immunologically cross-reactive plasma membrane proteins, of Mr 80,000 and Mr 210,000, have been purified to apparent homogeneity from sperm of the sea urchin Strongylocentrotus purpuratus. ...Purification includes a combination of antibody and wheat germ agglutinin affinity chromatography. The two proteins have similar but not identical amino acid compositions; however, their carbohydrate composition differs substantially. After purification, the Mr 210,000 protein binds to both living eggs and isolated egg jelly in a species-specific manner, but the Mr 80,000 protein does not. The inactivity of the Mr 80,000 protein could be due to denaturation during purification. The data are consistent with a model in which the Mr 210,000 protein acts as a jelly receptor in the sperm membrane, promoting the ion movements necessary to initiate the sperm acrosome reaction.
Three overlapping cDNA clones that hybridized to a v-ros probe were isolated from a cDNA library constructed from chicken kidney mRNA. Sequence analysis of these clones showed that they were all ...derived from c-ros mRNA. Using hybridization probes synthesized from the cDNA clones, a c-ros mRNA transcript of approximately 8.3 kb was detected in chicken kidney RNA, but not in chick embryo fibroblast RNA. The amino acid sequence predicted from the cDNA sequence indicates that the carboxyl terminus of the chicken c-ros protein contains 58 amino acids which are not present in v-ros. The predicted amino acid sequence of the chicken c-ros protein differs by 25% from that of its closest known human counterparts within the tyrosine protein kinase catalytic domain, and by 66% downstream of this domain. Despite these differences, both the chicken and human amino acid sequences share a potential site of tyrosine phosphorylation near their carboxyl termini that is absent from v-ros.
A method is described for isolating preparative quantities of plasma membranes from sea urchin sperm. The final membrane fraction is homogeneous by sucrose density sedimentation and is enriched in ...adenylate cyclase as well as in the four glycoproteins accessible to radioiodination of intact sperm. The electrophoretic profiles of sperm membranes from three sea urchin species are very similar. The membrane preparation consists primarily of sealed vesicles which release carboxyfluorescein when exposed to detergents or distilled water. Ninety-two percent of the
125I-labeled vesicle material binds to wheat germ lectin columns, suggesting a right-side-out orientation. The isolated sperm membrane vesicles exhibit species specific adhesion to the surfaces of sea urchin eggs; this adhesion is blocked by pretreatment of the vesicles with trypsin or egg jelly. This method will be useful for isolating biologically active sperm membrane components involved in sperm-egg recognition during fertilization.
The egg jelly-induced acrosome reaction is inhibited by polyclonal antibodies raised against either of two S. purpuratus sperm-membrane proteins, of Mr 80 and 210 kD. Although the two antigens used ...have dissimilar CNBr peptide maps, antisera produced against each of them cross-react with both proteins. Inhibition of the egg jelly-induced acrosome reaction by the antisera is bypassed by a combination of the ionophores monensin and A23187. This result, along with data showing that the antisera inhibit egg jelly-induced uptake of 45Ca2+, suggests that the antisera may block both Ca2+ uptake and Na+/H+ exchange in the sperm. The acrosome reaction blockage appears to be caused by the same component of the polyclonal sera responsible for cross-reaction; consequently, these antisera cannot be used to determine whether one or both of the cross-reacting proteins modulate a critical step in the acrosome reaction.
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