Small-angle X-ray scattering and in silico modeling approaches for the accurate functional annotation of an LysR-type transcriptional regulator.

Xylella fastidiosa is a xylem-limited, Gram-negative phytopathogen responsible for economically relevant crop diseases. Its genome was thus sequenced in an effort to characterize and understand its metabolism and pathogenic mechanisms. However, the assignment of the proper functions to the identified open reading frames (ORFs) of this pathogen was impaired due to a lack of sequence similarity in the databases. In the present work, we used small-angle X-ray scattering and in silico modeling approaches to characterize and assign a function to a predicted LysR-type transcriptional regulator in the X. fastidiosa (XfLysRL) genome. XfLysRL was predicted to be a homologue of BenM, which is a transcriptional regulator involved in the degradation pathway of aromatic compounds. Further functional assays confirmed the structural prediction because we observed that XfLysRL interacts with benzoate and cis,cis-muconic acid (also known as 2E,4E-hexa-2,4-dienedioic acid; hereafter named muconate), both of which are co-factors of BenM. In addition, we showed that the XfLysRL protein is differentially expressed during the different stages of X. fastidiosa biofilm formation and planktonic cell growth, which indicates that its expression responds to a cellular signal that is likely related to the aromatic compound degradation pathway. The assignment of the proper function to a protein is a key step toward understanding the cellular metabolic pathways and pathogenic mechanisms. In the context of X. fastidiosa, the characterization of the predicted ORFs may lead to a better understanding of the cellular pathways that are linked to its bacterial pathogenicity.

Characterization of the human dynein light chain Rp3 and its use as a non-viral gene delivery vector.

Dynein light chains mediate the interaction between the cargo and the dynein motor complex during retrograde microtubule-mediated transport in eukaryotic cells. In this study, we expressed and characterized the recombinant human dynein light chain Rp3 and developed a modified variant harboring an N-terminal DNA-binding domain (Rp3-Db). Our approach aimed to explore the retrograde cell machinery based on dynein to enhance plasmid DNA (pDNA) traffic along the cytosol toward the nucleus. In the context of non-viral gene delivery, Rp3-Db is expected to simultaneously interact with DNA and dynein, thereby enabling a more rapid and efficient transport of the genetic material across the cytoplasm. We successfully purified recombinant Rp3 and obtained a low-resolution structural model using small-angle X-ray scattering. Additionally, we observed that Rp3 is a homodimer under reducing conditions and remains stable over a broad pH range. The ability of Rp3 to interact with the dynein intermediate chain in vitro was also observed, indicating that the recombinant Rp3 is correctly folded and functional. Finally, Rp3-Db was successfully expressed and purified and exhibited the ability to interact with pDNA and mediate the transfection of cultured HeLa cells. Rp3-Db was also capable of interacting in vitro with dynein intermediate chains, indicating that the addition of the N-terminal DNA-binding domain does not compromise its function. The transfection level observed for Rp3-Db is far superior than that reported for protamine and is comparable to that of the cationic lipid Lipofectamine™. This report presents an initial characterization of a non-viral delivery vector based on the dynein light chain Rp3 and demonstrates the potential use of modified human light chains as gene delivery vectors.

Uric acid and acute kidney injury in high-risk patients for developing acute kidney injury undergoing cardiac surgery: A prospective multicenter study.

PURPOSE: It is unclear whether preoperative serum uric acid (SUA) elevation may play a role in the development of acute kidney injury (AKI) associated with cardiac surgery (CSA-AKI). We conducted a cohort study to evaluate the influence of preoperative hyperuricemia on AKI in patients at high risk for developing SC-AKI. DESIGN: Multicenter prospective international cohort study. SETTING: Fourteen university hospitals in Spain and the United Kingdom. PARTICIPANTS: We studied 261 consecutive patients at high risk of developing CSA-AKI, according to a Cleveland score ≥ 4 points, from July to December 2017. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: AKIN criteria were used for the definition of AKI. Multivariable logistic regression models and propensity score-matched pairwise analysis were used to determine the adjusted association between preoperative hyperuricemia (≥7 mg/dL) and AKI. Elevated preoperative AUS (≥7 mg/dL) was present in 190 patients (72.8%), whereas CSA-AKI occurred in 145 patients (55.5%). In multivariable logistic regression models, hyperuricemia was not associated with a significantly increased risk of AKI (adjusted Odds Ratio [OR]: 1.58; 95% confidence interval [CI]: 0.81-3; P = .17). In propensity score-matched analysis of 140 patients, the hyperuricemia group experienced similar adjusted odds of AKI (OR 1.05, 95%CI 0.93-1.19, P = .37). CONCLUSIONS: Hyperuricemia was not associated with an increased risk of AKI in this cohort of patients undergoing cardiac surgery at high risk of developing CSA-AKI.

Tris[2-(1,3-thiazol-2-yl-κN)-1H-benzimidazole-κN3]zinc(II) dinitrate ethanol hemisolvate monohydrate at 100 K.

The Zn(II) center in the dicationic complex of the title compound, [Zn(C(10)H(7)N(3)S)(3)](NO(3))(2)·0.5C(2)H(5)OH·H(2)O, is in a distorted octahedral environment with imperfect noncrystallographic C(3) symmetry. Each 2-(1,3-thiazol-2-yl)-1H-benzimidazole ligand coordinates in a bidentate manner, with the Zn-N(imidazole) bond lengths approximately 0.14 Å shorter than the Zn-N(thiazole) bond lengths. Charge-assisted hydrogen bonds connect cations, anions and water molecules. A lattice void is occupied by an ethanol solvent molecule disordered about a crystallographic inversion center and π-stacking is observed between one type of symmetry-related benzene rings.

(1S,2S,6R,7aR)-2-Benzyl-1,6-dihy-droxy-hexa-hydro-pyrrolizin-3-one.

In the title compound, C(14)H(17)NO(3), the dihedral angles show that the H atoms at two stereocenters are in a trans-diaxial configuration. In the crystal, the molecules are linked by O-H⋯O hydrogen bonds. The absolute configuration of the molecule has been established on the basis of refinement of the Hooft and Flack parameters.

(1S,2R,6R,7aS)-1,2,6-Trihy-droxy-hexa-hydro-1H-pyrrolizin-3-one.

In the title compound, C(7)H(11)NO(4), prepared via a Morita-Baylis-Hillman adduct, the five-membered ring bearing three O atoms approximates to a twisted conformation, whereas the other ring is close to an envelope, with a C atom in the flap position. The dihedral angle between their mean planes (all atoms) is 23.11 (9)°. The new stereocenters are created in a trans-diaxial configuration. In the crystal, O-H⋯O and O-H⋯(O,O) hydrogen bonds link the mol-ecules, generating a three-dimensional network. A weak C-H⋯O inter-action also occurs.

(1S,2E,6R,7aR)-1,6-Dihy-droxy-2-(4-nitro-benzyl-idene)-2,3,5,6,7,7a-hexa-hydro-1H-pyrrolizin-3-one.

The crystal structure of the title compound, C(14)H(14)N(2)O(5), contains two distinct conformers in the asymmetric unit. The compound has three defined stereocenters, two of them contiguous, and a C=C double bond with an E conformation. The stereocenters exhibit the same chirality in both conformers, with significant differences in the conformation of the five-membered rings of the pyrrolizine unit (both either in a twist or in an envelope form) and in the dihedral angles between the corresponding mean planes and the benzene rings. A prominent feature is a change from almost coplanar rings in one conformer to a new conformation in the second conformer, in which the mean plane of a five-membered ring is almost perpendicular to the benzene ring, with a dihedral angle 87.19 (8)°; the corresponding angle in the first conformer is 14.02 (10)°. In the crystal, molecules are linked by O-H⋯O and C-H⋯O hydrogen bonds. Crystallographic data were essential to confirm the configuration of the double bond, which was unclear from the available two-dimensional NMR data. In addition, reliable Flack and Hooft parameters were obtained, allowing for the correct absolute structure to be determined.

(1S,2E,6R,7aR)-2-Benzyl-idene-1,6-dihy-droxy-2,3,5,6,7,7a-hexa-hydro-1H-pyrrolizin-3-one.

In the title compound, C(14)H(15)NO(3), the conformation of the double bond was determined to be E, confirming the result obtained from two-dimensional NMR data. The five-membered rings of the pyrrolizine unit exhibit C-envelope conformations, with C atoms displaced from the mean planes formed by the remaining rings atoms by 0.1468 (15) and 0.5405 (17) Å. The mean planes of these rings (through all ring atoms) have a dihedral angle of 49.03 (10)°. In the crystal, mol-ecules are linked by O-H⋯O hydrogen bonds. The absolute configuration of the mol-ecule was established, as judged by the, as judged by the obtained values for the Hooft and Flack parameters.

Chain dynamics of poly(ethylene-alt-propylene) melts by means of coarse-grained simulations based on atomistic molecular dynamics.

We present coarse-grained molecular dynamics simulations of poly(ethylene-alt-propylene) (PEP) melts, ranging in chain length from about N(e) (the entanglement length) to N=6N(e). The coarse-grained parameters, potential of mean force and bare friction, were determined from fully atomistic molecular dynamics simulations carried out on a PEP cell containing 12 chains of 80 monomers each and subjected to periodic boundary conditions. These atomistic simulations were previously validated by means of extensive neutron scattering measurements. Uncrossability constrains were also introduced in the coarse-grained model to prevent unphysical bond crossing. The coarse-grained simulations were carried out at 492 K and focus on chain dynamics. The results obtained were analyzed in terms of Rouse coordinates and Rouse correlators. We observe deviations from Rouse behavior for all chain lengths investigated, even when the chain stiffness is incorporated in the Rouse model. These deviations become more important as the chain length increases. The general scenario emerging from the results obtained is that the deviations from Rouse-like behavior are due to correlations among the forces acting upon a chain bead, which seem to be related with the constraint of uncrossability among the chains. As consequence, nonexponentiality of the Rouse correlators and mode- and time-dependent friction are observed. It seems that, in the molecular weight explored, these effects still give not raise to reptation behavior but to a crossover regime between Rouse and reptation. On the other hand, the results obtained are in qualitative agreement with those expected from the so-called generalized Rouse models, based on memory function formalisms.

[Mortality following cardiac surgery in the National Health Service Hospitals of the Community of Valencia in 2007: a descriptive analysis]. / Análisis descriptivo de mortalidad en cirugía cardiaca en los hospitales públicos de la Comunidad Valenciana en el año 2007.

OBJECTIVE: To analyze clinical records of cardiac surgery patients in an attempt to identify factors associated with mortality in the postoperative critical care units of the public health service hospitals in the Community of Valencia, Spain, in 2007. METHODS: Retrospective study of cases from January 1, 2007 to December 31, 2007. The charts of all patients who underwent cardiac surgery with or without extracorporeal circulation were reviewed. A data collection protocol was followed to obtain information on age, sex, body mass index (BMI), presurgical risk factors, type of surgery, duration of extracorporeal circulation, duration of ischemia, cause of death, and length of stay in the postoperative critical care unit. RESULTS: The study population consisted of 2113 patients at 5 public hospitals; 124 patients (70 men, 54 women) died. The mean (SD) age was 70 (9.43) years (range, 36-91 years). The mean BMI was 28.19 kg/m2 (maximum, 42 kg/m2). The mean Euroscore was 21.92 (maximum, 94.29). Hypertension was present as a preoperative risk factor in most patients (74.2%); dyslipidemia was present in 51.6%, diabetes mellitus in 38.7%, stroke in 73%, and renal failure in 2.4%. It was noteworthy was that the group who underwent coronary revascularization had the highest mortality rate (nearly 35% of the 124 patients). The next highest mortality rate (19.4%) was in patients who had combined procedures (valve repair or substitution plus coronary revascularization). Mortality was 18.5% in the group undergoing aortic valve surgery and 11.3% in those undergoing mitral valve surgery. The mean duration of extracorporeal circulation was 148.63 minutes. The mean duration of myocardial ischemia was 94.91 minutes. The most frequent cause of death was cardiogenic shock (54.8%). This was followed by distributive shock (29.8%) and hemorrhagic shock (8.9%). The mean length of stay in the postoperative critical care unit was 13.6 days. Overall mortality was 5.87%. CONCLUSIONS: The highest mortality rate among cardiac surgery patients in postoperative critical care units in hospitals in the Community of Valencia in 2007 was in patients who underwent coronary revascularization. The most prevalent preoperative risk factor was hypertension. Cardiogenic shock and distributive shock were the most frequent causes of death in these patients. A system for classifying risk is needed in order to predict mortality in critical care units and improve perioperative care.

Oleoylethanolamide exerts partial and dose-dependent neuroprotection of substantia nigra dopamine neurons.

Oleoylethanolamide (OEA), agonist of nuclear PPAR-alpha receptors and antagonist of vanilloid TRPV1 receptors, has been reported to show cytoprotective properties. In this study, OEA-induced neuroprotection has been tested in vitro and in vivo models of 6-OHDA-induced degeneration of substantia nigra dopamine neurons. First, PPAR-alpha receptors were confirmed to be located in the nigrostriatal circuit, these receptors being expressed by dopamine neurons of the substantia nigra, and intrinsic neurons and fibers bundles of the dorsal striatum. In the substantia nigra, their location was confined to the ventral tier. The in vitro study showed that 1 microM OEA exerted a significantly neuroprotective effect on cultured nigral dopamine neurons, effects following U-shaped dose-response curves. Regarding the in vivo study, rats were locally injected with OEA into the right striatum and vehicle into the left striatum 30 min before 6-OHDA-induced striatal lesion. In the short term, signals of heme oxygenase-1 (oxidation marker, 24 and 48 h post-lesion) and OX6 (reactive microglia marker, 96 h post-lesion) were found to be significantly less intense in the striatum pretreated with 5 microM OEA. In the long term (1 month), reduction in striatal TH and synaptophysin was less intense whether the right striatum was pretreated with 5 microM OEA, and nigral TH+ neuron death was significantly reduced after pretreatment with 1 and 5 microM OEA. In vivo effects also followed U-shaped dose-response curves. In conclusion, OEA shows U-shaped partial and dose-dependent neuroprotective properties both in vitro and in vivo models of substantia nigra dopamine neuron degeneration. The occurrence of U-shaped dose-response relationships normally suggests toxicity due to high drug concentration or that opposing intracellular pathways are activated by different OEA doses.

Grafts of extra-adrenal chromaffin cells as aggregates show better survival rate and regenerative effects on parkinsonian rats than dispersed cell grafts.

The objective was to discern the neuroregenerative effect of grafts of extra-adrenal cells of the Zuckerkandl's paraganglion (ZP) in the nigrostriatal circuit, by using the retrograde model of parkinsonism in rats. The antiparkinsonian efficacy of two types of grafting procedures was studied (cell aggregates vs. dispersed cells), and GDNF and TGFbeta(1) (dopaminotrophic factors) as well as dopamine presence in extra-adrenal tissue was analyzed. Extra-adrenal chromaffin cells are noradrenergics, tissue dopamine is low, and they express both GDNF and TGFbeta(1). Grafts of cell aggregates, not of dispersed cells, exerted a trophic regeneration of the host striatum, leading to amelioration of motor deficits. Sprouting of spared dopaminergic fibers within the striatum, reduction of dopamine axon degeneration, and/or enhanced phenotypic expression of TH would explain striatal regeneration. Grafted cells as aggregates showed a better survival rate than dispersed cells, and they express higher levels of GDNF. Higher survivability and GDNF content together with the neurorestorative and dopaminotrophic action of both GDNF and TGFbeta(1) could account for striatal recovery and functional amelioration after grafting ZP cell aggregates. Finally, nigral degeneration and partial degeneration of ventral tegmental area were not precluded after transplantation, indicating that the trophic effect of grafts was local within the host striatum.

Gene-sized macronuclear DNA molecules are clustered in micronuclear chromosomes of the ciliate Oxytricha nova.

Following the sexual phase of its life cycle, the hypotrichous ciliate Oxytricha nova transforms a copy of its chromosomal micronucleus into a macronucleus containing short, linear DNA molecules with an average size of 2.2 kilobase pairs. In addition, more than 90% of the DNA sequences in the micronuclear genome are eliminated during this process. We have examined the organization of macronuclear DNA molecules in the micronuclear chromosomes. Macronuclear DNA molecules were found to be clustered and separated by less than 550 base pairs in two cloned segments of micronuclear DNA. Recombinant clones of two macronuclear DNA molecules that are adjacent in the micronucleus were also isolated and examined by DNA sequencing. The two macronuclear DNA molecules were found to be separated by only 90 base pairs in the micronuclear genome.

Detection of the presence of refined hazelnut oil in refined olive oil by fluorescence spectroscopy.

The fluorescence spectroscopy technique has been tested as regards its ability to differentiate between refined hazelnut and olive oils. Classification of these oils based on their excitation-emission fluorescence spectra data (spectral range 300-500 nm of the excitation spectra at lambdaem=655 and spectral range 650-900 of the emission spectra at lambdaex=50 nm) was performed using principal component analysis and artificial neural networks. Both methods provided good discrimination between the refined hazelnut and olive oils. The results have also pointed out the possibilities of a spectrofluorimetric method joined to multivariate analysis, to differentiate refined oils, and even to detect the presence of refined hazelnut oils in refined olive oils at percentages higher than 9%.

Changes induced by UV radiation during virgin olive oil storage.

The effects of UV radiation on the chemical and sensory characteristics of virgin olive oils (cv. Arbequina and Picual) were assessed. Even small doses of UV radiation induced oxidation of the virgin olive oil samples. Total phenols and fatty acids contents decreased during the process as well as the intensity of the bitter and fruity sensory attributes, while the intensity of the rancid sensory attribute notably increased. Acetaldehyde, 2-butenal, 2-pentenal, octane, octanal, hexanal, nonanal, and 2-decenal were the volatile compounds most affected, showing an important increase during the irradiation process. Nonanal, hexanal, and pentanal showed high correlation with the rancid sensory attribute (90%, 86%, and 86%, respectively). 2-Decenal and nonanal concentrations allowed us to predict the alteration level of the samples by mean of multiple Ridge regression.

Isolation and nucleotide sequence of the gene encoding the XamI DNA methyltransferase of Xanthomonas campestris pv. amaranthicola.

The gene (xamIM) encoding the DNA methyltransferase of the XamI restriction-modification system from Xanthomonas campestris pv. amaranithicola (M.XamI) has been cloned in Escherichia coli and its nucleotide sequence determined. The sequence predicts a protein of 527 amino acids that contains nine conserved motifs characteristic of DNA amino methyltransferases. In fact, M.XamI shows significant similarity with N6-adenine methyltransferases of the gamma group of amino methyltransferases, including M.SalI (from the isoschizomeric SalI restriction-modification system) and M.TaqI (the only N6-adenine methyltransferase for which a three-dimensional structure is available). M.XamI and M.SalI share two highly conserved regions within the C-terminal domain, one of which aligns with one of the DNA recognition loops proposed for M.TaqI. Analysis of the chromosomal DNA adjacent to xamIM led to the identification of an additional ORF (275 codons), downstream, in the same transcriptional orientation. Although some limited similarities between the SalI restriction enzyme and the product deduced from this ORF were found, the clone carrying xamIM did not express the expected endonuclease function.

A scheme of combined oral contraceptives for women more than 40 years old.

OBJECTIVE: To study whether the addition of estrogen to the 7 hormone-free days of a combined oral contraceptive (OC) cycle improves the symptomatology in perimenopausal women with climacteric complaints. DESIGN: A total of 56 women in their forties presenting with mood disorders and/or hot flashes were included in this randomized double-blind study. Symptoms were evaluated using the Greene test. Subjects were allocated into two groups: 23 women received an OC containing 20 microg of ethinyl-estradiol and 150 mg of desogestrel for 21 days and then 7 placebo tablets (placebo group); the other 33 women received 21 tablets with the same hormone combination, followed by 2 placebo tablets and 5 ethinyl-estradiol tablets of 10 microg each (estrogen group). After three cycles, symptoms were reassessed. RESULTS: Symptoms were similar in the two groups at the start of the study. Three months later, vasomotor symptoms in the placebo group dropped from 3.3 +/- 1.7 to 1.7 +/- 1.8, and in the estrogen group, from 3.0 +/- 1.7 to 0.7 +/- 0.9 (p < 0.04). Similarly, symptoms of depression fell from 8.8 +/- 4.0 to 6.7 +/- 3.9 in the placebo group and from 10.3 +/- 3.5 to 3.8 +/- 2.9 in the estrogen group (p < 0.002). Somatic symptoms fell with placebo from 10.9 +/- 5.3 to 7.4 +/- 5.4, and with estrogen, from 9.7 +/- 4.9 to 4.0 +/- 2.5 (p < 0.03). Sexual dysfunction as measured by the Greene Scale (loss of sexual interest) also improved more in women who received additional estrogen: 2.0 +/- 0.9 to 0.5 +/- 0.9 vs. 1.8 +/- 1.2 to 1.2 +/- 1.2, p < 0.03. Anxiety symptoms improved in both groups but without any significant difference between them. CONCLUSIONS: Adding 5 days of estrogen to the classic contraceptive scheme improves the climacteric symptoms of perimenopausal women who use OCs.

Authentication of vegetable oils by chromatographic techniques.

Food authentication has been evolving continually to situations that were basically governed by a global market trend. Analytical techniques have been developed or modified to give plausible solutions to the devious adulterations at each moment. Classical tests have largely been replaced with newer technical procedures, most of which are based on gas chromatography, with some being based on high-performance liquid chromatography. Determination of trans-fatty acid and sterolic composition, together with sterol-dehydration products, have been used most frequently used to detect contamination and adulteration. Sophisticated new adulterations, e.g., olive oil with hazelnut oil, represent a new challenge for the next millennium, although suggestive proposals for detecting these kinds of adulterations are emerging with the contribution of databases and mathematical algorithms.

Interpretation of Fourier transform Raman spectra of the unsaponifiable matter in a selection of edible oils.

The unsaponifiable matter of edible oils is a source of information for their characterization and authentication. FT-Raman spectroscopy has been applied with success to the determination of the spectra of the unsaponifiable matter of varietal olive oils as well as other refined and crude edible oils. The spectra of the major unsaponifiable series of compounds (squalene, sterolic, and terpenic alcoholic fractions), together with beta-carotene and lutein, have been used to explain the most prominent bands found in the spectra of the unsaponifiable matter of 15 edible oil samples. The order of the scattering intensities of the varietal olive oils agrees with the results obtained by chromatography. An unsupervised multivariate statistical analysis of selected bands points out differences between olive oils and the other seed oils and also among varietal virgin olive oils.

Detection of rancid defect in virgin olive oil by the electronic nose.

A sensor array of 32 conducting polymer sensors has been used to detect the rancid defect in virgin olive oils. A training set, composed of admixtures of a Portuguese virgin olive oil with different percentages (0-100%) of a rancid standard oil, was used for the selection of the best sensors classifying correctly the samples. Information on volatile compounds responsible for rancidity and the sensory evaluation of samples by assessors were used for explaining the mathematical selection of sensors. A tentative calibration, using unsupervised procedures (PCA and MDS) and a nonlinear regression, was carried out, with the training set, and later confirmed with a test set with which rancid commercial samples of different varieties were used to spike a Greek extra virgin olive oil at low levels of rancidity (0.5-6%).