A genome-wide nanotoxicology screen of Saccharomyces cerevisiae mutants reveals the basis for cadmium sulphide quantum dot tolerance and sensitivity.

The use of cadmium sulphide quantum dots (CdS QDs) is increasing, particularly in the electronics industry. Their size (1-10 nm in diameter) is, however, such that they can be taken up by living cells. Here, a bakers' yeast (Saccharomyces cerevisiae) deletion mutant collection has been exploited to provide a high-throughput means of revealing the genetic basis for tolerance/susceptibility to CdS QD exposure. The deletion of 112 genes, some associated with the abiotic stress response, some with various metabolic processes, some with mitochondrial organization, some with transport and some with DNA repair, reduced the level of tolerance to CdS QDs. A gene ontology analysis highlighted the role of oxidative stress in determining the cellular response. The transformation of sensitive mutants with centromeric plasmids harbouring DNA from a wild type strain restored the wild type growth phenotype when the complemented genes encoded either HSC82, DSK2 or ALD3. The use of these simple eukaryote knock-out mutants for functional toxicogenomic analysis will inform studies focusing on higher organisms.

Nutritional status and airflow obstruction: two independent contributors to CO diffusing capacity impairment in COPD.

BACKGROUND: The association between weight loss and Chronic Obstructive Pulmonary Disease (COPD) has been recognised from many years. Based on the evidence that nutritional status reflects metabolic disturbances in COPD, the relationship between body mass index (BMI), severity of airflow obstruction and CO diffusing capacity (DL(CO)), that is the functional hallmark of emphysema, is relevant to the management of COPD phenotypes. METHODS: We reviewed 104 patients with COPD (82 males), aged 66 +/- 9 years (mean +/- SD). Height averaged 165 +/- 8 cm, weight 71 +/- 16 Kg, FEV1 50 +/- 18 (% of predicted), RV 169 +/- 49%, and DL(CO) 56 +/- 26%. Multiple linear regression was performed using BMI, FEV1 and RV, as explanatory variables for DL(CO). Patients were also classified into four groups according to BMI < or = 18.5 (low), > 18.5 and < or = 25 (ideal), > 25 and < or = 30 (overweight), > 30 (obese), and post-bronchodilator FEV1 < 50%. Using this categorisation, a two-factor analysis of variance, testing for interaction and main effects (BMI and FEV1) was performed as confirmatory analysis for the association between BMI (kg/m2), FEV1% and DL(CO)%. RESULTS: FEV1 and BMI were significantly and independently associated to DL(CO) according to the equation: DL(CO) = -18.32 + 0.65 x FEV1 + 1.59 x BMI (R2 = 0.40, p < 0.0001). The contribution of RV % to DL(CO) % was largely non-significant (p = 0.16). A close relationship was found between BMI (kg/m2) and DL(CO) %, for all of the four BMI groups segregated by post-bronchodilator FEV1 %, (p < .0001). No interaction was found between these two factors (p = 0.30). CONCLUSION: Nutritional status as assessed by BMI contributes substantially to impairment of DL(CO) independently of the severity of airflow obstruction. This data confirms the association between emphysematous process and weight loss in advanced COPD, independent of the airflow obstruction severity.

Targeted DNA integration within different functional gene domains in yeast reveals ORF sequences as recombinational cold-spots.

The efficiency of gene targeting within different segments of genes in yeast was estimated by transforming yeast cells with double-stranded integrative plasmids, bearing functional gene domains [promoter (P), ORF (O) and terminator (T)] derived from the common genetic markers HIS3, LEU2, TRP1 and URA3. Transformation experiments with circular plasmids carrying a single gene domain demonstrated that the 5' and 3' flanking DNA regions (P and T) of the HIS3 and URA3 genes are preferred as sites for plasmid integration by several fold over the corresponding ORFs. Moreover, when plasmids bearing combinations of two or three regions were linearized to target them to a specific site of integration, three of the ORFs were found to be less preferred as sites for plasmid integration than their corresponding flanking regions. Surprisingly, in up to 50% of the transformants obtained with plasmids that had been linearized within coding sequences, the DNA actually integrated into neighbouring regions. Almost the same frequencies of ORF mis-targeting were obtained with plasmid vectors containing only two functional domains ("PO" or "OT") of the gene URA3, demonstrating that this event is not the consequence of competition between homologous DNA regions distal to the ORF. Therefore, we suggest that coding sequences could be considered to be "cold spots" for plasmid integration in yeast.

Knowledge of the Bacillus subtilis genome: impacts on fundamental science and biotechnology.

The advent of genomics has greatly influenced fundamental and applied microbiology. This has become paradigmatic in the case of Bacillus subtilis, a primary model bacterium for research and biotechnology. Indeed, mining its genome has provided more fruitful information than classical approaches would have yielded in a longer period of time. Through advanced analysis of its genome and transcriptome, fundamental discoveries dealing with the informational architecture of the B. subtilis chromosome, as well as with the elucidation of its pathway-level regulation of gene expression, have been achieved. The possibility of performing a complete metabolic manipulation of the secretory pathway of Bacillus is promising important biotechnological fallouts. Similar emphasis exists for the possibility of controlling the cell in the formation of biofilms with specific physical and chemical characteristics. At the theoretical level, the new concept of genetic superinformation has been formulated and its analytical approach implemented, while the understanding of the minimal genetic requirements for the existence of a reproducing bacterial cell is being tackled. In summary, the impact of the B. subtilis genome has philosophically revolutionised the way that basic knowledge is translated into applied microbiology and biotechnology, making this bacterium the workhorse of post-genomic microbiology.

Levodropropizine does not affect P0.1 and breathing pattern in healthy volunteers and patients with chronic respiratory impairment.

To evaluate whether the peripherally acting antitussive levodropropizine could affect the respiratory drive and the breathing pattern, we performed a double-blind, randomised, cross-over trial in 12 healthy volunteers and 12 patients with chronic respiratory impairment associated with chronic obstructive pulmonary disease. Levodropropizine 6% drops (at the recommended dose for adults) or placebo were administered orally t.i.d. for 10 consecutive administrations. Mouth occlusion pressure (P0.1), minute ventilation (V(e)), tidal volume (V(t)), respiratory rate (RR), mean inspiratory flow (V(t)/T(i)), end-tidal CO(2) (EtCO(2)), oxygen saturation (SaO(2)), forced expiratory volume in 1 s (FEV(1)), and the response to a hypercapnic stimulus were measured before and 1 h after the first and the last drug administration. Levodropropizine did not modify P0.1 in basal conditions and after a hypercapnic stimulus, either in healthy volunteers or in patients. In parallel, levodropropizine did not significantly affect V(t), RR, V(e), V(t)/T(i) and EtCO(2) in both the populations. Minor changes were induced by levodropropizine on SaO(2) in healthy volunteers, which despite a statistical difference, were too low to gain a clinical significance. These results confirmed the respiratory safety of levodropropizine 6% drops administered at the recommended dosage either in healthy volunteers or patients with chronic respiratory impairment.

Secondary DNA structure analysis of the coding strand switch regions of five Leishmania major Friedlin chromosomes.

As part of the EULEISH international genome project, a region of 74,674 nucleotides from chromosome 21 of Leishmania major Friedlin was subcloned and sequenced; and 31 new coding sequences were predicted. Of particular interest was a unique coding strand switching region covering 1.6 kb of DNA; and this was subjected to further investigation. Bioinformatic analysis of this region revealed an unusually high AT composition, a lack of putative hairpins and a strong curvature of the DNA in agreement with the structural characteristics of similar regions of other Leishmania chromosomes. These observations and a comparison with the secondary DNA structure of four other Leishmania chromosomes and chromosomes of different organisms could suggest a functional role of this region in transcription and mitotic division.

Abc protein transport of MRI contrast agents in canalicular rat liver plasma vesicles and yeast vacuoles.

The mechanism of excretion into bile of hepatospecific magnetic resonance imaging (MRI) contrast media employed labeled Gd-reagents EOB.DTPA, BOPTA, B 20790 (iopanoate-linked), and B 21690 (glycocholate-linked) for measurement in rat liver canalicular plasma membrane vesicles and yeast vacuoles. The presence of ATP gave threefold greater transport of B 20790 and B 21690 than of EOB.DTPA and BOPTA. In yeast vacuoles the ATP stimulatory effect was eightfold with B 20790 and fivefold greater for B 21690, whereas in YCF1- or YLLO115w-deleted yeast cells the transport was significantly reduced and absent from double mutants, YCF1 and YLLO15w. The transport was similar in wild-type and deletant cells for B 21690; taurocholate gave 85% inhibition. These data suggest that bilary secretion of structurally related MRI agents depend on molecular structure. The findings are suggestive as of possible value for clinical diagnosis of inherited hyperbilirubinemias and other liver disorders.

Erectile dysfunction in men with obstructive sleep apnea: an early sign of nerve involvement.

Erectile dysfunction (ED) is common in men with obstructive sleep apnea (OSAS) but no completely convincing hypotheses about the underlying pathogenic mechanisms have been published in the literature. The aims of the present study were to assess the presence of ED in a group of OSAS patients without daytime respiratory failure and to determine whether this dysfunction was related to peripheral nerve involvement. Evaluation of the bulbocavernosus reflex (BCR) and the somato-sensory evoked potentials of pudendal nerve (PSEPs), the most widely established method of documenting pudendal neuropathies as being the cause of impotence, was performed in 25 patients. Data on BCR were compared with those of 25 healthy males volunteers matched for age. BCR was altered in 17 patients: in 6 it was elicited while in 11 it had a prolonged latency and reduced amplitude. Patients with altered BCR presented an higher AHI, an higher percentage of sleep time spent with SaO2 <90% (TST90) and a lower daytime PaO2. Six patient had clinically silent neurophysiological signs of mild polyneuropathy. The degree of OSAS and gas exchange alteration was more severe in patients with polyneuropathy than in those with isolated BCR alteration. ED is a common finding in OSAS patients and this alteration seems to be related to a nerve dysfunction. The development of nerve dysfunction is associated with a more severe degree of OSAS and nocturnal hypoxia.

The products of YCF1 and YLL015w (BPT1) cooperate for the ATP-dependent vacuolar transport of unconjugated bilirubin in Saccharomyces cerevisiae.

Since bilirubin-like pigments are present in the environment as degradation products of heme-containing proteins, yeast could have developed a detoxifying system to transport these compounds into their vacuoles. Vacuoles from Saccharomyces cerevisiae showed an ATP-dependent, saturative transport of unconjugated bilirubin (UCB) that was reduced by 60% and 40% in YCF1 and YLL015w-deleted cells, respectively; the double deletant showed no UCB uptake. Conversely, the transport of bile acids (taurocholate) was comparable in wild and deleted stains. These data identify YCF1 and YLL015w, named BPT1 (Bile Pigment Transporter), as the genes responsible for ATP-dependent UCB transport in yeast. Since YCF1 and YLL015w are rather homologous with multidrug resistant proteins (MRPs), they also suggest the involvement of this class of transporters in the ATP-dependent transport of unconjugated bilirubin.

Involvement of the inverted repeat of the yeast 2-micron plasmid in Flp site-specific and RAD52-dependent homologous recombination.

Site-specific recombination within the Saccharomyces cerevisiae 2-micron DNA plasmid is catalyzed by the Flp recombinase at specific Flp Recognition Target (FRT) sites, which lie near the center of two precise 599-bp Inverted Repeats (IRs). However, the role of IR DNA sequences other than the FRT itself for the function of the Flp reaction in vivo is not known. In the present work we report that recombination efficiency differs depending on whether the FRT or the entire IR serves as the substrate for Flp. We also provide evidence for the involvement of the IR in RAD52-dependent homologous recombination. In contrast, the catalysis of site-specific recombination between two FRTs does not require the function of RAD52. The efficiency of Flp site-specific recombination between two IRs cloned in the same orientation is about one hundred times higher than that obtained when only the two FRTs are present. Moreover, we demonstrate that a single IR can activate RAD52-dependent homologous recombination between two flanking DNA regions, providing new insights into the role of the IR as a substrate for recombination and a new experimental tool with which to study the molecular mechanism of homologous recombination.

Pulmonary function and complications following chemotherapy and stem cell support in breast cancer.

Pulmonary complications are frequent in patients treated with high-dose chemotherapy and autologous bone marrow transplantation for breast cancer or other solid tumours. This study analyses the development of lung toxicity, changes in respiratory function and occurrence of clinical symptoms in a group of 24 patients (mean age 46+/-7 yrs) who underwent high-dose sequential chemotherapy (HDS) with autologous peripheral blood stem cell (PBSC) support for high risk breast cancer. Clinical examination, chest radiography and lung function tests were performed before the HDS and 1 and 3 months following transplantation. Only one patient developed acute interstitial pulmonary disease which resolved after prednisone therapy. No patients developed infectious complications after transplantation. Baseline respiratory function was normal for most of the parameters. Only lung diffusing capacity of the lung for carbon monoxide (TL,CO) and maximal inspiratory pressure were below the normal range. Following PBSC transplantation only one patient had an altered vital capacity while 72.3% of patients had reduced TL,CO values at 1 month and 54.5% at 3 months after transplantation. Maximal expiratory flow at 25% forced vital capacity, TL,CO and maximal expiratory pres-sure were significantly reduced after 1 month but recovered slightly by 3 months. Arterial oxygen tension between baseline and both follow-up evaluations declined significantly in patients seropositive for human cytomegalovirus. It is concluded that this high-dose sequential chemotherapy regimen is acceptably safe since no pulmonary related mortality or respiratory infectious complications were observed. The only lung function alteration induced was an isolated diffusing capacity of the lung for carbon monoxide impairment, clinically negligible and partially recovered within 3 months.

Identification of chronic heart failure patients at risk of Cheyne-Stokes respiration.

Chronic heart failure (CHF) patients frequently show sleep-disordered breathing consisting of periodic breathing (PB) and Cheyne-Stokes respiration (CSR) with central sleep apnoea (CSA). Since the diagnosis of sleep-disordered breathing, in CHF patients, can be made only by means of full polysomnography, the aim of the present study was to evaluate whether or not daytime respiratory function can identify patients at risk of nocturnal PB and/or CSR/CSA. Twenty-seven patients (mean age 54 +/- 8.5 yrs), eight New York Heart Association Functional Class (NYHAFC) II, 17 NYHAFC III and two NYHAFC IV, with severe cardiac failure (cardiac output 2.0 +/- 0.66 L.min-1, ejection fraction 22.5 +/- 5.77%, pulmonary capillary wedge/pressure 23 +/- 9.05 mmHg). Mouth occlusion pressure (P0.1)/maximal inspiratory pressure (MIP) was significantly higher in patients with nocturnal CSR/CSA (5.04 +/- 1.49 versus 3.24 +/- 2.13%, analysis of variance (ANOVA) 0.03), whereas their arterial carbon dioxide tension (Pa,CO2) was significantly lower (4.15 +/- 0.56 (31.2 +/- 4.23 mmHg) versus 4.67 +/- 0.53 kPa (35.1 +/- 4 mmHg), ANOVA 0.02). Logistic regression analysis demonstrated that CSR/CSA occurrence may be predicted by daytime measurement of P0.1/MIP and Pa,CO2 (p = 0.04 and 0.01 respectively; odds ratio 1.93 and 0.76 respectively). The sensitivity was 70%, specificity 76.5%, false positive rate 36.4%, false negative rate 18.8%, positive predictive value 71.4% and negative predictive value 85%. This model seems useful for predicting respiratory pattern changes in chronic heart failure patients and the authors suggest that polysomnography be performed only in high-risk patients, saving costs and the resources of sleep laboratories.

Disruption of seven hypothetical aryl alcohol dehydrogenase genes from Saccharomyces cerevisiae and construction of a multiple knock-out strain.

By in silicio analysis, we have discovered that there are seven open reading frames (ORFs) in Saccharomyces cerevisiae whose protein products show a high degree of amino acid sequence similarity to the aryl alcohol dehydrogenase (AAD) of the lignin-degrading fungus Phanerochaete chrysosporium. Yeast cultures grown to stationary phase display a significant aryl alcohol dehydrogenase activity by degrading aromatic aldehydes to the corresponding alcohols. To study the biochemical and the biological role of each of the AAD genes, a series of mutant strains carrying deletion of one or more of the AAD-coding sequences was constructed by PCR-mediated gene replacement, using the readily selectable marker kanMX. The correct targeting of the PCR-generated disruption cassette into the genomic locus was verified by analytical PCR and by pulse-field gel electrophoresis (PFGE) followed by Southern blot analysis. Double, triple and quadruple mutant strains were obtained by classical genetic methods, while the construction of the quintuple, sextuple and septuple mutants was achieved by using the marker URA3 from Kluyveromyces lactis, HIS3 from Schizosaccharomyces pombe and TRP1 from S. cerevisiae. None of the knock-out strains revealed any mutant phenotype when tested for the degradation of aromatic aldehydes using both spectrophotometry and high performance liquid chromatography (HPLC). Specific tests for changes in the ergosterol and phospholipids profiles did not reveal any mutant phenotype and mating and sporulation efficiencies were not affected in the septuple deletant. Compared to the wild-type strain, the septuple deletant showed an increased resistance to the anisaldehyde, but there is a possibility that the nutritional markers used for gene replacement are causing this effect.

The relation between behavior problems and peer preference in different classroom contexts. Conduct Problems Prevention Research Group.

This study tested two alternative hypotheses regarding the relations between child behavior and peer preference. The first hypothesis is generated from the person-group similarity model, which predicts that the acceptability of social behaviors will vary as a function of peer group norms. The second hypothesis is generated by the social skill model, which predicts that behavioral skill deficiencies reduce and behavioral competencies enhance peer preference. A total of 2895 children in 134 regular first-grade classrooms participated in the study. Hierarchical linear modeling was used to compare four different behaviors as predictors of peer preference in the context of classrooms with varying levels of these behavior problems. The results of the study supported both predictive models, with the acceptability of aggression and withdrawal varying across classrooms (following a person-group similarity model) and the effects of inattentive/hyperactive behavior (in a negative direction) and prosocial behavior (in a positive direction) following a social skill model and remaining constant in their associations with peer preference across classrooms. Gender differences also emerged, with aggression following the person-group similarity model for boys more strongly than for girls. The effects of both child behaviors and the peer group context on peer preference and on the trajectory of social development are discussed.

A 2-microm DNA-based marker recycling system for multiple gene disruption in the yeast Saccharomyces cerevisiae.

A molecular FRT (Flp recombinase recognition target)-based cassette system for multiple gene disruption in the yeast Saccharomyces cerevisiae was developed. FRT DNA sequences were designed with different core mutations and subsequently cloned in direct orientation upstream and downstream of a marker gene to serve as template for the amplification of a set of different gene disruption cassettes. After each disruption, the marker can be easily eliminated from its integration site by in vivo site-specific recombination between the two identical, mutated FRT sequences flanking the marker, leaving behind one FRT sequence with a particular point mutation. Since recombination between two FRTs with a different core mutation is extremely rare, the possibility of chromosome rearrangements, due to site-specific recombination between residual FRTs, is very low. In strains containing 2-microm ([cir+]) the site-specific reaction is catalysed by the endogenous Flp gene product, whereas in strains without 2-microm ([cir0]), the FLP gene is carried on the cassette, together with the marker gene. This system can be applied for haploid and diploid [cir+] and [cir0] strains.

Fractal properties of DNA walks.

We describe two dimensional DNA walks, and analyze their fractal properties. We show results for the complete genome of S. cerevisiae. We find that the mean square deviation of the walks is superdifussive, corresponding to a fractal structure of dimension lower than two. Furthermore, the coding part of the genome seems to have smaller fractal dimension, and longer correlations, than noncoding parts.

Synthesis and secretion of Providencia rettgeri and Escherichia coli heterodimeric penicillin amidases in Saccharomyces cerevisiae.

The Providencia rettgeri and Escherichia coli pac genes encoding heterodimeric penicillin G amidases (PAC) were successfully expressed in Saccharomyces cerevisiae. Furthermore, these recombinant enzymes are secreted from the yeast cell into the medium which is in contrast to bacterial hosts, where the enzymes are retained in the periplasm. Contrary to the P. rettgeri PAC-encoding gene, the E. coli pac is poorly expressed in yeast. The highest yield of P. rettgeri PAC was obtained with a multi-copy plasmid, resulting in of 1500units per liter. This yield is higher by an order of magnitude than that obtained in the best recombinant bacterial expression system. The recombinant P. rettgeri enzyme is only partially and selectively O-glycosylated. Only every sixth or seventh alpha-subunit is glycosylated, while the beta-subunit is not glycosylated at all. N-Glycosylation has not been detected.

Visual hallucinations in the 19th century: research in a medical archive.

The authors have gathered and analyzed the visual hallucinations described in the mid- to late-19th century from archived medical records of the former psychiatric hospital "Osservanza" in Imola, northern Italy. Though the investigation was not intended as a statistical survey, the principal aim being to classify the hallucinations according to their outward characteristics, the authors have tried to locate the possible sources of these phenomena in folklore and religious iconography.

The development of hyperventilation in patients with chronic heart failure and Cheyne-Strokes respiration: a possible role of chronic hypoxia.

AIM: To analyze the relationship between daytime respiratory and cardiac function in patients with compensated chronic heart failure (CHF) with and without periodic breathing (PB) or Cheyne-Stokes respiration (CSR). PATIENTS: We studied 132 patients (female, 13%; mean age, 53+/-8 years; body mass index, 25.9+/-3.5 kg/m2; left ventricular ejection fraction <40%; 23% in New York Heart Association class I, 43% in class II, and 34% in class III-IV). METHODS: Measurement of pulmonary function and blood gases, hemodynamic evaluation, analysis of breathing profile, echocardiography, recording of ECG, beat-to-beat arterial oxygen saturation, and respiration during spontaneous breathing. RESULTS: Fifty-eight percent of patients showed PB or CSR. Patients with PB or CSR have greater cardiac function impairment. Mean values of lung volumes and PaO2 were similar in the three groups of patients considered. In contrast, patients with PB or CSR had an increased minute ventilation and reduced PaCO2 values. Interestingly, patients with PB or CSR had lower values of arterial content of O2 and systemic oxygen transport (SOT) than patients with a normal breathing pattern (SOT, 394+/-9.8, 347+/-9.6, 438+/-11 mL of O2/min/m2, respectively; analysis of variance p<0.001). Weak correlations were found among lung volumes, blood gases, and cardiac function parameters: ie, vital capacity was correlated inversely with pulmonary capillary wedge pressure (PCWP) (-0.25; p<0.05); PaCO2 with PCWP (r=0.26; p<0.05), lung-to-ear circulation time (LECT) (r=-0.4; p<0.05), SOT (r=-0.33; p<0.0001), and cardiac index (CI) (r=0.27; p=0.003). Multiple regression analyses showed that arterial PCO2 was significantly correlated with SOT, LECT, and CI (r=0.51; r2=0.26; p<0.000001); the correlation became stronger considering only CSR patients (r=0.64; r2=0.4; p<0.001). CONCLUSIONS: Our study shows that patients with daytime breathing disorders have chronic hypocapnia. A reduced SOT may be one of the stimuli determining increased minute ventilation in these patients.