Orthogonal combinatorial mutagenesis: a codon-level combinatorial mutagenesis method useful for low multiplicity and amino acid-scanning protocols

We describe here a method to generate combinatorial libraries of oligonucleotides mutated at the codon-level, with control of the mutagenesis rate so as to create predictable binomial distributions of mutants. The method allows enrichment of the libraries with single, double or larger multiplicity of amino acid replacements by appropriate choice of the mutagenesis rate, depending on the concentration of synthetic precursors. The method makes use of two sets of deoxynucleoside-phosphoramidites bearing orthogonal protecting groups [4,4'-dimethoxytrityl (DMT) and 9-fluorenylmethoxycarbonyl (Fmoc)] in the 5' hydroxyl. These phosphoramidites are divergently combined during automated synthesis in such a way that wild-type codons are assembled with commercial DMT-deoxynucleoside-methyl-phosphoramidites while mutant codons are assembled with Fmoc-deoxynucleoside-methyl-phosphoramidites in an NNG/C fashion in a single synthesis column. This method is easily automated and suitable for low mutagenesis rates and large windows, such as those required for directed evolution and alanine scanning. Through the assembly of three oligonucleotide libraries at different mutagenesis rates, followed by cloning at the polylinker region of plasmid pUC18 and sequencing of 129 clones, we concluded that the method performs essentially as intended.

Biochemical characterization of profilin from seeds of Phaseolus vulgaris L

The isoform composition of the 14.4 kDa profilin polypeptide was analyzed in seeds, leaves, flowers, roots and root-nodules from Phaseolus vulgaris L. Isoforms of pIs approximately 4.4-5 were present in all the tissues analyzed. The biochemical features of the protein present in seed tissue were determined. Seed profilin bound to Phenyl-Sepharose under low salt conditions which suggested a hydrophobic interaction; however, it was not associated with microsomal membranes nor it partitioned as a hydrophobic protein in Triton X-114. Fractions eluting from poly-L-proline or Phenyl-Sepharose columns contained well detectable amounts of profilin but no actin, suggesting that most of the protein was not present as profilactin in the seed. However, seed profilin appeared to be in some kind of complex since several molecular weight species were observed on native gels. In addition, profilin was found preferentially in the embryo axis and light microscopic immunolocalization showed a cytoplasmic distribution in this tissue.

Immediate allergic reactions to cephalosporins: cross-reactivity and selective responses

BACKGROUND

After penicillins, cephalosporins are the most important beta-lactams inducing IgE-mediated reactions. Responses may be selective or cross-reactive with common beta-lactam determinants. Unlike determinants derived from benzylpenicillin, cephalosporin allergenic determinants have not been properly identified, even though a wide variety of these beta-lactams is currently used.

OBJECTIVE

We sought to evaluate the IgE response in subjects with immediate allergic reactions to injectable cephalosporins and to assess their reactivity to different penicillins and cephalosporins.

METHODS

We studied 30 subjects with immediate reactions to one or more of the following cephalosporins: ceftriaxone, cefotaxime, ceftazidime, and cefuroxime. Skin tests and in vitro-specific IgE antibody assays were performed for major and minor determinants of penicillin G, amoxicillin, and ampicillin, as well as for the culprit cephalosporins. Responses to cephalosporins other than the culprit ones were also studied by using skin testing.

RESULTS

Twenty-six patients (group A, 86.7%) displayed skin test and RAST negativity to penicillin determinants and skin test positivity to cephalosporins, with RAST confirmation in 9 patients. Four subjects (group B, 13.3%) had a positive response to penicillin determinants. In group A two patterns of reactivity were observed: one characterized by a response only to the culprit cephalosporin (n = 15, 57.7%) and the other by positive responses to different cephalosporins, including the responsible cephalosporins (n = 11, 42. 3%).

CONCLUSION

Most patients with a history of immediate reactions to cephalosporins are sensitized to determinants generated only by cephalosporins (group A), although a small percentage react to penicillin determinants (group B). Some patients from group A responded only to the culprit cephalosporin, but others reacted to different cephalosporins. These findings can be explained in terms of either selective response to unique determinants or cross-reactivity.

The cylindrical inclusion gene of Turnip mosaic virus encodes a pathogenic determinant to the Brassica resistance gene TuRB01

The viral component of Turnip mosaic virus (TuMV) determining virulence to the Brassica napus TuRB01 dominant resistance allele has been identified. Sequence comparisons of an infectious cDNA clone of the UK 1 isolate of TuMV (avirulent on TuRB01) and a spontaneous mutant capable of infecting plants possessing TuRB01 suggested that a single nucleotide change in the cylindrical inclusion (CI) protein coding region (gene) of the virus was responsible for the altered phenotype. A second spontaneous mutation involved a different change in the CI gene. The construction of chimeric genomes and subsequent inoculations to plant lines segregating for TuRB01 confirmed the involvement of the CI gene in this interaction. Site-directed mutagenesis of the viral coat protein (CP) gene at the ninth nucleotide was carried out to investigate its interaction with TuRB01. The identity of this nucleotide in the CP gene did not affect the outcome of the viral infection. Both mutations identified in the CI gene caused amino acid changes in the C terminal third of the protein, outside any of the conserved sequences reported to be associated with helicase or cell-to-cell transport activities. This is the first example of a potyvirus CI gene acting as a determinant for a genotype-specific resistance interaction.

The Bcg host-resistance gene

In the mouse, resistance and susceptibility to intracellular growth of mycobacteria in macrophages is controlled by the Bcg (Nramp1) gene, which has been cloned and shown to encode a macrophage phagosomal membrane protein with a putative transporter function. In the homologous human NRAMP1 gene, a total of 11 polymorphisms have been identified, which are being used to test for the linkage of NRAMP1 alleles with human responses to mycobacteria, including susceptibility to tuberculosis and leprosy, as well as BCG immunotherapy in bladder cancer.

[Effect of mitomycin C on corneal endothelium cells. In vitro study]

PURPOSE

Mitomycin C is an antibiotic with a demonstrated antiproliferative capacity as an inhibitor of fibroblastic cells proliferation. Its use has been extended in glaucoma surgery. In the present study, we evaluated mitomycin C effect on cell culture monolayer of rabbit corneal endothelium.

METHODS

The source of corneal endothelium for cell culture was New Zealand albino rabbit eyes. Desegregation of cells was carried out with mechanic and enzymatic dissociation from corneal endothelium and Descemet membrane. Culture medium was EMEM. Three treatment groups of plates were exposed to three different concentrations of mitomycin C 2x10(-3) mg/ml, 2x10(-2) mg/ml and 2x10(-1) mg/ml. Control and witness plate groups were also established. The morphometric study was performed through quantitative analysis with a video system connected to the light microscope.

RESULTS

Different morphological changes related with cell size, cytoplasm and dyeing were seen at the morphological study and several degenerative signs were established indicating cellular death and a very decrease of the cellular population. In the groups treated with minimal dose (2x10(-3) mg/ml) and 3 days evolution time, cellular population was 434 cels/mm(2), 7 evolution days group cell density was 300.97cels/mm(2), and at 14 days it was 201.88 cels/mm(2). The percentage of survival in all the groups of treated cells was under 50%.

CONCLUSIONS

Mitomycin C in concentrations and exposure time as used in this study has a potent lethal effect on this cellular type that compromises to a greater or smaller extent their function and integrity.

[Caroli's syndrome. Report of a case beginning in childhood with favorable course]

Caroli's disease is a rare entity that is included in the fibropolycystic abnormalities of the bile ducts. Ultrasonographic patterns consist of evident dilatation of the bile ducts. Although it is thought to be a congenital disease, it usually presents in young adults and few cases have been reported in children. We present the case of a 10-year-old boy with Caroli's syndrome (Caroli's disease, congenital hepatic fibrosis and polycystic renal disease). Evolution was favorable.

ArF excimer laser irradiation of human dentin

BACKGROUND AND OBJECTIVE

The use of excimer lasers for treatment of dental hard tissues has considerable potential because the combined characteristics of low wavelength and short pulse result in limited heat diffusion and, therefore, tissue ablation without the problems of collateral damage. To date, there are relatively few published studies concerning the effects of excimer laser irradiation on dental hard tissues. Thus the present study was conducted to examine the morphological changes in tooth dentin subsequent to ArF excimer laser irradiation.

STUDY DESIGN/MATERIALS AND METHODS

The morphologic changes induced in normal, nondiseased human dentin following irradiation by an ArF excimer laser at fluences ranging from 1 to 4 J/cm2 and the number of laser pulses ranging from 50 to 1,000 were evaluated by scanning electron microscopy.

RESULTS

Two modes of ablation, photochemical at low fluences and thermal at high fluences, were observed. A fluence of 1 J/ cm2 when combined with 50 or 100 pulses produced a uniform ablation of the dentin surface without signs of tissue melting. At fluences > 1.5 J/cm2, the thermal mode of ablation was more efficient at removing intertubular dentin than peritubular dentin. Further, when compared to the lower fluences, the higher settings produced a rougher ablation crater surface. Additionally, the higher fluences produced surface melting with each pulse and sealing of exposed dentinal tubules after irradiation with 100-300 laser pulses.

CONCLUSIONS

The photochemical and thermal mechanisms of tooth dentin ablation were identified based on significant differences in tissue morphology following laser irradiation. The rates of tissue ablation and the observed morphologic changes indicate that the ArF excimer laser could be useful for caries removal and sealing of exposed dentinal tubules.

Microbiological quality control study of "all-in-one" total parenteral nutrition admixtures

A microbiological quality control study of parenteral nutrition (PN) is presented. The study was carried out in the Pharmacy and Microbiology Services of the Hospital de la Santa Creu i Sant Pau (Barcelona, Spain) from April 1991 to May 1998 and represents more than 25,000 lipid-containing PN admixtures prepared during that 7-year period. A randomized sampling procedure according to the cumulative sum control charts was performed and a 0.45-microm membrane filtration method was used as the microbiological test. Validation showed that the method is sensitive for sterility tests. Bacterial growth was observed on 59 filters (4.58% of the samples). A second control was made for these positive outcomes, and bacterial growth was found in only two cases. The patients' clinical history was reviewed and no relation between the microorganisms of the nutrition and the results obtained from blood cultures was observed. The quality control study revealed a low incidence of contamination in our PN preparation process.

Pathogenic significance of methicillin resistance for patients with Staphylococcus aureus bacteremia

To assess whether methicillin resistance is a microbial characteristic associated with deleterious clinical outcome, we performed a cohort study on 908 consecutive episodes of Staphylococcus aureus bacteremia and a case-control study involving 163 pairs of patients matched for preexisting comorbidities, prognosis of the underlying disease, length of hospitalization, and age. Of 908 bacteremic episodes, 225 (24.8%) were due to methicillin-resistant S. aureus (MRSA). Multivariate analysis did not reveal that methicillin resistance was an independent predictor for mortality when shock, source of bacteremia, presence of an ultimately or rapidly fatal underlying disease, acquisition of the infection in an intensive care unit (ICU), inappropriate empirical therapy, female sex, and age were taken into account. Nonetheless, methicillin resistance was an independent predictor for shock. The case-control study could not confirm that shock was linked to MRSA when prior antimicrobial therapy, inappropriate treatment, ICU residence, and female sex were considered. Our data suggest that cohort studies tend to magnify the relationship of MRSA with clinical markers of microbial pathogenicity and that this effect is a shortcoming of these kind of studies that is caused by inadequate control for underlying diseases.

[The prognostic factors of invasive pulmonary aspergillosis in patients with chronic pneumopathy]

OBJECTIVES

a) To determine in patients with chronic respiratory disease the risk factors for death due to semi-invasive and invasive pulmonary aspergillosis (SIPA), and b) to describe the clinical features of SIPA in such patients.

METHOD

Twenty-one patients with chronic respiratory disease were enrolled (9 with chronic obstructive pulmonary disease, 2 asthmatics and 3 with bronchiectasis, 5 with post-tubercular sequelae and 2 mixed cases). A diagnosis of SIPA was established in our hospital when, in a patient with a clinical picture consistent with such a diagnosis, the fungus was isolated in bronchial secretions or parenchymal pulmonary specimens were obtained during autopsy.

RESULTS

The most common symptoms were dyspnea (81%), cough (67%) and expectoration (62%) increasing over the levels usual for patients with chronic respiratory disease. Hemoptysis was present in only 14%. Eight patients (38%) died as a result of SIPA. A comparison of those surviving and non-surviving patients revealed that the latter had significantly higher LDH levels and white cell counts, and significantly lower total plasma protein and platelet counts.

CONCLUSIONS

a) Low protein levels and high LDH levels and white cell counts with thrombopenia are indicators of poor prognosis in chronic respiratory disease patients with SIPA, and b) such patients do not usually present signs or symptoms that lead to a suspicion of SIPA given that such signs are typical of failing compensatory mechanisms in the disease itself.

[Pneumonia caused by Haemophilus influenzae. Study in a series of 58 patients]

Haemophilus influenzae tends to form part of the usual respiratory flora in adults, especially if they have a chronic underlying disease or are smokers. Pneumonia due to H. influenzae is frequently involved in respiratory infections and its level of resistance to ampicillin has remained stable over the last five years. Most of the literature on the subject was published more than 10 years ago. In this study, we describe the clinical features and evolution of 58 adult patients admitted to hospital for pneumonia due to H. influenzae over a 2-year period, with this group accounting for 6.5% of all the patients admitted with pneumonia during this time period. The etiological diagnosis was made using a good quality sputum sample. Forty patients (69%) were male. The mean age (+/- SD) of the group was 67 (+/-16.8) years and all the patients had at least one underlying disease. The mean duration of the symptoms was 6.7 days. All patients presented an increase in the quantity or purulence of the sputum. On admittance, respiratory failure was present in 52 patients (90%). Gram-negative coccus-bacilli were observed in the direct sputum test and H. influenzae grew in the culture. In two cases, H. influenzae was recovered from the blood culture and in one from bronchial aspiration obtained through bronchoscopy. Another pathogen was identified in 28 patients (48%). In 21 it was another pyogenic bacteria (15 S. pneumoniae, 4 M. catharralis, 1 K. pneumoniae, 1 E. coli), an atypical microorganism in 5 (3 C. pneumoniae, 2 C. burnetii) and a respiratory virus in 2 (syncytial and influenza A). Atypical bacteria and respiratory virus were detected using serological techniques. The radiographic infiltrate was unilobar in 54 of the 58 patients and all showed an alveolar pattern. The empirical treatment included the administration of a third generation cephalosporin (or a fluoroquinolone in patients allergic to penicillin). The evolution was favorable in all the cases in which H. influenzae was the only pathogen or was accompanied by an atypical microorganism or a respiratory virus. Four patients with mixed bacterial pneumonia died (2 S. pneumoniae, 1 E. coli and 1 M. catharralis). The study indicates that pneumoniae due to H. influenzae affects a population with an underlying disease, preferably pulmonary, that it has a longer clinical period than that for pneumococcal pneumonia, that it is slightly bacteremic and, that, usually, it evolves benignly with a low mortality.

Changes of environment and darkness enhance the NADPH-diaphorase staining in the rat paraventricular nucleus

Nitric oxide (NO) plays an important role in the maintenance of autonomic homeostasis of the body. NO-producing neurons are activated in the brain during exposure to different levels of environmentally produced stimulations. These facts prompted the authors to investigate the levels of activation of NO-producing neurons of the paraventricular nucleus of the hypothalamus (PVN) following change of environment and darkness. Cryostat sections were cut and processed for the histochemical detection of the NADPH-diaphorase (ND)-activity. Following change of the environment and darkness for 12 and 24 h, statistical analysis displayed a significant increase in the number of ND-neurons, especially in the posterior magnocellular and the lateral parvicellular subdivisions of the PVN. These data indicate that the ND-neurons of the PVN are influenced by changes of the environment and darkness.

[Electroencephalographic and hemodynamic monitoring at various desflurane concentrations]

OBJECTIVES

To assess the electroencephalographic patterns and hemodynamic changes produced by desflurane at 0.5, 1 and 1.5 MAC.

MATERIAL AND METHODS

Twenty-four patients undergoing gynecological surgery under general anesthesia were enrolled prospectively. We monitored electroencephalographic (EEG) patterns and hemodynamic parameters as well as inspired and expired desflurane fractions. Anesthetic induction was with 2 mg/kg of propofol, 2 to 3 mg/kg of fentanyl and 0.1 mg/kg vecuronium. Spectral edge frequency (SEF90) and the EEG delta ratio were recorded along with mean systolic and diastolic pressures, heart rate, oxygen saturation and expired CO2 fraction during induction, intubation, 5 min after intubation and at 0.5, 1 and 1.5 MAC during weaning from anesthesia and extubation.

RESULTS

Blood pressure fell significantly at 1.5 MAC and increased when anesthesia was withdrawn; heart rate did not change significantly. SEF90 and the delta ratio changed, however, at each phase. SEF90 fell notably at the moment of induction but gradually increased, rising upon intubation, 5 min later, at 0.5 MAC and upon withdrawal of anesthesia. A significant decrease in SEF90 appeared when 1.5 MAC was reached, related to achievement of a deeper plane of anesthesia.

CONCLUSIONS

Automated EEG processing can provide a good measure of depth of anesthesia, as it reflects significant changes related to level of anesthesia at each phase. These differences are not always observable with routine monitoring of hemodynamic parameters.