General method for plasmid construction using homologous recombination

We describe a general method for plasmid assembly that uses yeast and extends beyond yeast-specific research applications. This technology exploits the homologous recombination, double-stranded break repair pathway in Saccharomyces cerevisiae to join DNA fragments. Synthetic, double-stranded "recombination linkers" were used to "subclone" a DNA fragment into a plasmid with > 80% efficiency. Quantitative data on the influence of DNA concentration and overlap length on the efficiency of recombination are presented. Using a simple procedure, plasmids were shuttled from yeast into E. coli for subsequent screening and large-scale plasmid preps. This simple method for plasmid construction has several advantages. (i) It bypasses the need for extensive PCR amplification and for purification, modification and/or ligation techniques routinely used for plasmid constructions. (ii) The method does not rely on available restriction sites, thus fragment and vector DNA can be joined within any DNA sequence. This enables the use of multifunctional cloning vectors for protein expression in mammalian cells, other yeast species, E. coli and other expression systems as discussed. (iii) Finally, the technology exploits yeast strains, plasmids and microbial techniques that are inexpensive and readily available.     

Sentences over Integral Domains and Their Computational Complexities

LetRbe a Hilbertian domain and letKbe its fraction field. Letψ(x₁, …, x_n, y) be a quantifier free arithmetical formula overR. We may also takeψ(x₁, …, x_n, y) to be an arithmetical formula overK[x₁, …, x_n] and write it asψ(y). In this paper we show that ifRhas enough non-units and x₁…x_n y ψ(x₁, …, x_n, y), called an ⁿ  sentence, is true inR, then y ψ(y) is true inK[x₁, …, x_n]. Also, ifR=K[T], whereKis an infinite integral domain andx₁…x_n y ψ(x₁, …, x_n, y)is true inR, then y ψ(y) is true inR[x₁, …, x_n]. These results are applied to find the upper and lower bounds of the time complexities of various decision problems on diophantine equations with parameters and arithmetical sentences. Some of the results are: 1. The decision problem of sentences and diophantine equations with parameters over the ring of integers of a global field are co-NP-complete. 2. The decision problem of sentences over the ring of integers of a global field is NP-complete. 3. LetKbe an infinite domain, the time complexities of the decision problems of equations with parameters and sentences over the polynomial ringK[t] are polynomial time reducible to factoring polynomials overK. 4. The decision problem of sentences over all algebraic integer rings is in P. 5. The decision problem of sentences over all integral domains with characteristic 0 is in P. 6. The time complexity of the decision problem of sentences over all integral domains is polynomial time reducible to factoring integers overZand factoring polynomials over finite fields.     

Finite element modeling of three-dimensional pulsatile flow in the abdominal aorta: relevance to atherosclerosis

The infrarenal abdominal aorta is particularly prone to atherosclerotic plaque formation while the thoracic aorta is relatively resistant. Localized differences in hemodynamic conditions, including differences in velocity profiles, wall shear stress, and recirculation zones have been implicated in the differential localization of disease in the infrarenal aorta. A comprehensive computational framework was developed, utilizing a stabilized, time accurate, finite element method, to solve the equations governing blood flow in a model of a normal human abdominal aorta under simulated rest, pulsatile, flow conditions. Flow patterns and wall shear stress were computed. A recirculation zone was observed to form along the posterior wall of the infrarenal aorta. Low time-averaged wall shear stress and high shear stress temporal oscillations, as measured by an oscillatory shear index, were present in this location, along the posterior wall opposite the superior mesenteric artery and along the anterior wall between the superior and inferior mesenteric arteries. These regions were noted to coincide with a high probability-of-occurrence of sudanophilic lesions as reported by Cornhill et al. (Monogr. Atheroscler. 15:13-19, 1990). This numerical investigation provides detailed quantitative data on hemodynamic conditions in the abdominal aorta heretofore lacking in the study of the localization of atherosclerotic disease.     

Experimental infection of domestic sheep with culture-derived Leishmania donovani promastigotes

Domestic sheep were intradermally inoculated with culture-derived stationary phase Leishmania donovani promastigotes. Sampling of site of inoculation, liver and spleen for 244 days showed that this parasite can stay alive in the skin for up to 28 days post-inoculation. Apart from pyrexia that was evident in all the animals for 42 days, no other symptoms of kala-azar were seen. No parasites were recovered from the visceral organs throughout the sampling period, suggesting that sheep are not susceptible to infection with L. donovani. It is therefore unlikely that sheep can be synanthropic reservoirs for this parasite.     

Effect of the administration of fish oil by gavage on activities of antioxidant enzymes of rat lymphoid organs

Expression of retinoblastoma (Rb) protein was immunohistochemically examined in laryngeal squamous cell neoplasias from 72 patients. Staining patterns were considered with reference to such prognostic factors as patient's age, histologic grade, tumour size and lymph node status, and 5-year survival rate. Rb protein negativity, either partial or complete, was noted in 28.8% of cases and was associated with a significantly lower 5-year survival rate, as well as with a higher likelihood of lymph node metastasis. This suggests that Rb alteration may be a prognostic indicator in patients with laryngeal carcinoma.     

Identification and characterization of the PutP proline permease that contributes to in vivo survival of Staphylococcus aureus in animal models

Staphylococcus aureus is an important pathogen of humans and other animals, causing bacteremia, abscesses, endocarditis, and other infectious syndromes. A signature-tagged mutagenesis (STM) system was adapted for use in studying the genes required for in vivo survival of S. aureus. An STM library was ultimately created in S. aureus RN6390, with Tn917 being used to create the transposon mutations. Pools of S. aureus RN6390 mutants were screened in mouse abscess, bacteremia, and wound infection models for growth attenuation after in vivo passage. One of the mutants that was identified displayed marked attenuation following large-pool screening in all three animal models, which was confirmed in bacteremia and endocarditis models of infection with a smaller pool of mutants. Sequence analysis of the entire open reading frame showed a 99% identity to the high-affinity proline permease (putP) gene characterized in another strain of S. aureus. In wound and murine abscess infection models, the putP mutant was approximately 10-fold more attenuated than was wild-type strain RN6390. Another S. aureus strain transduced with the putP mutation also displayed an attenuated phenotype after passage in the wound model. A [3H]proline uptake assay showed that less proline was specifically transported into the putP mutant than into strain RN6390. The reduced viability of the bacteria possessing the mutation in the S. aureus high-affinity proline permease suggests that proline scavenging by the bacteria is important for in vivo growth and proliferation and that analogs of proline may serve as potential antistaphylococcal therapeutic agents.