The mechanism and energetics of a ligand-controlled hydrophobic gate in a mammalian two pore channel.

In the last decade two-pore intracellular channels (TPCs) attracted the interest of researchers, still some key questions remain open. Their importance for vacuolar (plants) and endo-lysosomal (animals) function highlights them as a very attractive system to study, both theoretically and experimentally. Indicated as key players in the trafficking of the cell, today they are considered a new potential target for avoiding virus infections, including those from coronaviruses. A particular boost for theoretical examinations has been made with recent high-resolution X-ray and cryo-EM structures. These findings have opened the way for efficient and precise computational studies at the atomistic level. Here we report a set of multiscale-calculations performed on the mTPC1, a ligand- and voltage-gated sodium selective channel. The molecular dynamics and enhanced molecular dynamics simulations were used for a thorough analysis of the mammalian TPC1 behaviour in the presence and absence of the ligand molecule, with a special accent on the supposed bottleneck, the hydrophobic gate. Moreover, from the reconstructed free energy obtained from enhanced simulations, we have calculated the macroscopic conductance of sodium ions through the mTPC1, which we compared with measured single-channel conductance values. The hydrophobic gate works as a steric barrier and the key parameters are its flexibility and the dimension of the sodium first hydration shell.

A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds.

We present an on-line database of all-atom force-field parameters and molecular properties of compounds with antimicrobial activity (mostly antibiotics and some beta-lactamase inhibitors). For each compound, we provide the General Amber Force Field parameters for the major species at physiological pH, together with an analysis of properties of interest as extracted from µs-long molecular dynamics simulations in explicit water solution. The properties include number and population of structural clusters, molecular flexibility, hydrophobic and hydrophilic molecular surfaces, the statistics of intraand inter-molecular H-bonds, as well as structural and dynamical properties of solvent molecules within first and second solvation shells. In addition, the database contains several key molecular parameters, such as energy of the frontier molecular orbitals, vibrational properties, rotational constants, atomic partial charges and electric dipole moment, computed by Density Functional Theory. The present database (to our knowledge the first extensive one including dynamical properties) is part of a wider project aiming to build-up a database containing structural, physico-chemical and dynamical properties of medicinal compounds using different force-field parameters with increasing level of complexity and reliability. The database is freely accessible at http://www.dsf.unica.it/translocation/db/.

A mutation-based radiomics signature predicts response to imatinib in Gastrointestinal Stromal Tumors (GIST).

Objectives: To develop a mutation-based radiomics signature to predict response to imatinib in Gastrointestinal Stromal Tumors (GISTs). Methods: Eighty-two patients with GIST were enrolled in this retrospective study, including 52 patients from one center that were used to develop the model, and 30 patients from a second center to validate it. Reference standard was the mutational status of tyrosine-protein kinase (KIT) and platelet-derived growth factor α (PDGFRA). Patients were dichotomized in imatinib sensitive (group 0 - mutation in KIT or PDGFRA, different from exon 18-D842V), and imatinib non-responsive (group 1 - PDGFRA exon 18-D842V mutation or absence of mutation in KIT/PDGFRA). Initially, 107 texture features were extracted from the tumor masks of baseline computed tomography scans. Different machine learning methods were then implemented to select the best combination of features for the development of the radiomics signature. Results: The best performance was obtained with the 5 features selected by the ANOVA model and the Bayes classifier, using a threshold of 0.36. With this setting the radiomics signature had an accuracy and precision for sensitive patients of 82 % (95 % CI:60-95) and 90 % (95 % CI:73-97), respectively. Conversely, a precision of 80 % (95 % CI:34-97) was obtained in non-responsive patients using a threshold of 0.9. Indeed, with the latter setting 4 patients out of 5 were correctly predicted as non-responders. Conclusions: The results are a first step towards using radiomics to improve the management of patients with GIST, especially when tumor tissue is unavailable for molecular analysis or when molecular profiling is inconclusive.

Effects of abscisic acid on ethylene biosynthesis and perception in Hibiscus rosa-sinensis L. flower development.

The effect of the complex relationship between ethylene and abscisic acid (ABA) on flower development and senescence in Hibiscus rosa-sinensis L. was investigated. Ethylene biosynthetic (HrsACS and HrsACO) and receptor (HrsETR and HrsERS) genes were isolated and their expression evaluated in three different floral tissues (petals, style-stigma plus stamens, and ovaries) of detached buds and open flowers. This was achieved through treatment with 0.1 mM 1-aminocyclopropane-1-carboxylic acid (ACC) solution, 500 nl l(-1) methylcyclopropene (1-MCP), and 0.1 mM ABA solution. Treatment with ACC and 1-MCP confirmed that flower senescence in hibiscus is ethylene dependent, and treatment with exogenous ABA suggested that ABA may play a role in this process. The 1-MCP impeded petal in-rolling and decreased ABA content in detached open flowers after 9 h. This was preceded by an earlier and sequential increase in ABA content in 1-MCP-treated petals and style-stigma plus stamens between 1 h and 6 h. ACC treatment markedly accelerated flower senescence and increased ethylene production after 6 h and 9 h, particularly in style-stigma plus stamens. Ethylene evolution was positively correlated in these floral tissues with the induction of the gene expression of ethylene biosynthetic and receptor genes. Finally, ABA negatively affected the ethylene biosynthetic pathway and tissue sensitivity in all flower tissues. Transcript abundance of HrsACS, HrsACO, HrsETR, and HrsERS was reduced by exogenous ABA treatment. This research underlines the regulatory effect of ABA on the ethylene biosynthetic and perception machinery at a physiological and molecular level when inhibitors or promoters of senescence are exogenously applied.

Electronic and Optical Properties of Small Metal Fluoride Clusters.

We report a systematic investigation on the electronic and optical properties of the smallest stable clusters of alkaline-earth metal fluorides, namely, MgF2, CaF2, SrF2, and BaF2. For these clusters, we perform density functional theory (DFT) and time-dependent DFT (TDDFT) calculations with a localized Gaussian basis set. For each molecule ((MF2) n , n = 1-3, M = Mg, Ca, Sr, Ba), we determine a series of molecular properties, namely, ground-state energies, fragmentation energies, electron affinities, ionization energies, fundamental energy gaps, optical absorption spectra, and exciton binding energies. We compare electronic and optical properties between clusters of different sizes with the same metal atom and between clusters of the same size with different metal atoms. From this analysis, it turns out that MgF2 clusters have distinguished ground-state and excited-state properties with respect to the other fluoride molecules. Sizeable reductions of the optical onset energies and a consistent increase of excitonic effects are observed for all clusters under study with respect to the corresponding bulk systems. Possible consequences of the present results are discussed with respect to applied and fundamental research.

Molecular basis for the different interactions of congeneric substrates with the polyspecific transporter AcrB.

The drug/proton antiporter AcrB, which is part of the major efflux pump AcrABZ-TolC in Escherichia coli, is the paradigm transporter of the resistance-nodulation-cell division (RND) superfamily. Despite the impressive ability of AcrB to transport many chemically unrelated compounds, only a few of these ligands have been co-crystallized with the protein. Therefore, the molecular features that distinguish good substrates of the pump from poor ones have remained poorly understood to date. In this work, a thorough in silico protocol was employed to study the interactions of a series of congeneric compounds with AcrB to examine how subtle chemical differences affect the recognition and transport of substrates by this protein. Our analysis allowed us to discriminate among different compounds, mainly in terms of specific interactions with diverse sub-sites within the large distal pocket of AcrB. Our findings could provide valuable information for the design of new antibiotics that can evade the antimicrobial resistance mediated by efflux pump machinery.

Pulmonary hypertension following L-lysine ibuprofen therapy in a preterm infant with patent ductus arteriosus.

Patent ductus arteriosus is one of the most common congenital abnormalities found in premature infants. Ibuprofen, a nonsteroidal drug that is commonly used as an antipyretic, analgesic and anti-inflammatory agent, is also used to induce closure of symptomatic patent ductus arteriosus in preterm infants. Recently, we gave L-lysine ibuprofen to a preterm infant with respiratory distress to induce closure of a patent ductus arteriosus, and the infant experienced pulmonary hypertension. Only 3 cases of pulmonary hypertension following early administration of an ibuprofen solution buffered with tromethamine have previously been reported. However, this severe side effect has never been observed in multicentre, randomized, double-blind controlled trials, nor in recent reviews or meta-analyses of L-lysine ibuprofen use.

Lack of effect of dietary nucleotide supplementation on erythrocyte 2,3-diphosphoglycerate concentration. A study on preterm neonates.

BACKGROUND: Recently we demonstrated an increased 2,3-diphosphoglycerate (2,3-DPG) erythrocyte concentration in rat pups subjected to nucleotide-enriched artificial feeding. DESIGN: The present study was carried out to test the hypothesis that a possible increase in 2,3-DPG concentration can also be obtained in human neonates who are fed nucleotide-enriched formula. Preterm neonates born or referred to the neonatal intensive care unit of the G. Gaslini Hospital, Genoa University, with a gestational age >30 weeks and <37 weeks were enrolled in our randomized trial. Recruitment took place within 48-72 hours from birth. Only newborns of mothers deciding not to breast-feed were eligible to be randomized for the supplemented group (FN) or non-supplemented group (RF). Breast-fed newborns were considered the control group (C). The study window (for supplementation and blood samples) was restricted to the first two weeks following birth (from the 2nd (t1) to the 16th (t2) day of life). At the end of our study, only 21 neonates were eligible for statistical analysis. RESULTS: The stimulating action of dietary nucleotides on 2,3-DPG concentration failed to be demonstrated; increases in 2,3-DPG concentration that were observed in newborns fed with nucleotide supplemented formula (FN) were comparable to those observed in newborns fed with regular formula (RF) and breast-fed newborns. CONCLUSIONS: The EC recommendation for the amount of nucleotides allowed in formula milk does not seem to be high enough to have positive effects on 2,3-DPG synthesis. Whether this possible 'pharmacological' effect can be achieved by a higher intake of ingested nucleotides and/or a change in the proportions of single nucleotides contained in milk formulas remain interesting end points to be elucidated.

S100B protein levels in saliva: correlation with gestational age in normal term and preterm newborns.

OBJECTIVES: S100B is an acidic calcium-binding protein of the EF-hand family present in the central nervous system, where it is concentrated in glial cells. It has been suggested to act as a cytokine with neurotrophic effects at physiological concentrations. DESIGN AND METHODS: S100B concentration was assessed in saliva by western blot analysis and an immunoluminometric assay. A reference curve of the protein was established in 216 preterm and term newborns. RESULTS: S100B levels were significantly higher in saliva taken from the preterm group, and the highest S100B levels were found in newborns who were delivered in the earlier weeks of gestation, exhibiting a progressive decrease nearer to term. S100B concentration in saliva was correlated with gestational age (r = -0.69; P < 0.001). CONCLUSIONS: The present study offers data consistent with the putative neurotrophic role of S100B and suggests the usefulness of saliva in the clinical monitoring of S100B levels.

"Apple-peel" intestinal atresia, ocular anomalies, and microcephaly syndrome: brain magnetic resonance imaging study.

We report on a male child with "apple-peel" atresia associated with microcephaly and ocular anomalies. To date, no magnetic resonance imagings have been published. We report on the fourth reported case with this phenotype, but the first to be studied by brain magnetic resonance imaging.

Measurement of urinary S100B protein concentrations for the early identification of brain damage in asphyxiated full-term infants.

BACKGROUND: Perinatal asphyxia is a major cause of mortality and morbidity. To date there are no reliable methods to detect which infants will develop brain damage after asphyxia insult. We investigated whether measurements of urine levels of S100B in asphyxiated full-term newborns may be a useful tool for early detection of postasphyxia brain damage. METHODS: A prospective study of 38 infants with perinatal asphyxia and 96 control subjects, recruited at 3 tertiary departments of neonatology between April 1, 1999, and July 31, 2001. Routine laboratory variables, neurologic patterns, and urine concentrations of S100B protein were determined at 4 predetermined time points (first urination and 12, 24, and 72 hours after birth). The concentrations of S100B protein in urine were measured using an immunoluminometric assay. The results were correlated with the presence or absence of neurologic abnormalities at age 12 months. RESULTS: S100B protein levels were significantly higher in samples collected at all monitoring times from new-borns with abnormal neurologic findings on follow-up (first urination, 1.92 +/- 0.33 micro g/L; 12 hours, 2.78 +/- 1.71 micro g/L; 24 hours, 4.75 +/- 4.08 micro g/L; 72 hours, 5.93 +/- 1.63 micro g/L) than in samples from those without (first urination, 0.24 +/- 0.06 micro g/L; 12 hours, 0.13 +/- 0.06 micro g/L; 24 hours, 0.21 +/- 0.07 micro g/L; 72 hours, 0.12 +/- 0.04 micro g/L) or from healthy infants (first urination, 0.11 +/- 0.01 micro g/L; 12 hours, 0.12 +/- 0.03 micro g/L; 24 hours, 0.12 +/- 0.02 micro g/L; 72 hours, 0.12 +/- 0.02 micro g/L) (P<.001 for all). An S100B concentration cutoff of 0.28 micro g/L at first urination had a sensitivity of 100% and a specificity of 87.3% for predicting the development of abnormal neurologic findings on follow-up. The sensitivity and specificity of measurements obtained between 12 and 72 hours were up to 100% and 98.2%, respectively. CONCLUSION: Longitudinal S100B protein measurements in urine soon after birth are a useful tool to identify which asphyxiated infants are at risk of long-term neurologic sequelae.

Adrenomedullin increases in term asphyxiated newborns developing intraventricular hemorrhage.

OBJECTIVES: Adrenomedullin (AM) is a newly discovered vasodilator peptide that participates in the regulation of cerebral blood flow. The aim of this study was to investigate whether circulating AM was increased in infants with prenatal asphyxia who developed intraventricular hemorrhage (IVH). DESIGN AND METHOD: : A case-control study was performed on 40 full-term asphyxiated newborns: 20 developed IVH (group A) and 20 did not (group B). Forty term healthy newborns represented the control group. Biochemical laboratory parameters, neurological patterns, cerebral ultrasound scanning, and Doppler velocimetry were assessed at 12 and 72 h from birth. Plasma AM concentration was measured at 12 h from birth by means of a specific RIA. RESULTS: AM levels were significantly higher in group A (20.2 +/- 5.2 fmol/ml) than in group B (8.4 +/- 2.1 fmol/ml) or controls (9.3 +/- 2.6 fmol/ml). In asphyxiated newborns, AM concentration was correlated with middle cerebral artery PI value only in group B. CONCLUSIONS: Increased concentration of AM at 12 h from birth in asphyxiated newborns who later developed IVH suggests that this peptide may participate in the loss of cerebral vascular autoregulation in response to hypoxia and could be useful to discriminate, among newborns at risk, those with an adverse neurological outcome.

Levels of S100B protein are higher in mature human milk than in colostrum and milk-formulae milks.

BACKGROUND & AIMS: Human milk is believed to contain biological factors involved in the regulation of newborn growth, including brain development. Recently, it has also been shown to contain the calcium-binding S100B protein, regarded as a neurotrophic factor. The present study investigates the concentrations of this protein in colostrum, human milk at different levels of maturation and in milk-formulae. METHODS: Samples for S100B measurements were collected from human colostrum (on day 1 after birth), from transition milk (on post-delivery days 7 and 14) and from mature milk (on day 30 after delivery) in 14 healthy women and from 14 milk-formulae. The S100B protein levels were measured using a commercially available specific immunoluminometric assay. RESULTS: Mean S100B protein levels were significantly higher in mature human milk (117.9+/-36.7 microg/l) than in transition milk at 14 days (106.7+/-38.1 microg/l) and at 7 days (92.7+/-37.8 microg/l), colostrum (74.6+/-37.6 microg/l) or milk-formulae (24.8+/-19.5 microg/l) (P<0.001, for all). A correlation between human milk S100B levels and the gestational age at which samples were obtained was also found (r=0.39; P<0.01). CONCLUSIONS: These findings, possibly related to S100B's neurotrophic role, offers useful information to the investigation of the role of S100B protein in brain maturation.

Cholesterol oxidation in intravenous lipid emulsions: safety of preparations before and after experimental hyperoxia.

The aim of this preliminary study was to assess the possible presence of cholesterol oxidation products in 2 i.v. lipidic emulsions with different fatty acid compositions (long-chain triglyceride, medium-chain triglyceride-long-chain triglyceride). Because these emulsions are currently used in neonatal parenteral nutrition, their direct venous introduction might be potentially dangerous because of the possible atherogenic role of cholesterol oxidation products. The emulsions were analyzed when bottles were opened (ie, under normal condition of administration) and after a 12-hour direct experimental exposure to air and high (90%) oxygen concentrations. 7-Ketocholesterol and 5alpha-epoxycholesterol were chosen as markers of cholesterol oxidation and detected by gas chromatography-mass spectrometry of their trimethylsilyl ethers. The detected amounts were always very low and in some cases below the detection limit of the analytical method for the 2 cholesterol oxidation products (COPs; 0.1 and 0.3 microg/g of extracted lipids). Immediately after opening the bottles, their concentrations were lower in the emulsions containing the higher amounts of polyunsaturated fatty acids. Experimental hyperoxic exposure generally determined only a mild increase in the content of cholesterol oxidation biomarker, and after exposure to oxygen, the amounts of COPs were slightly higher than after exposure to air. The results of the present study are undoubtedly reassuring for the safety of neonates, although caution is always required when drawing conclusions from in vitro data.

Procalcitonin in detecting neonatal nosocomial sepsis.

OBJECTIVE: To investigate the accuracy of procalcitonin (PCT) as a diagnostic marker of nosocomial sepsis (NS) and define the most accurate cut-off to distinguish infected from uninfected neonates. SETTING: Six neonatal intensive care units (NICUs). PATIENTS: 762 neonates admitted to six NICUs during a 28-month observational study for whom at least one serum sample was taken on admission. MAIN OUTCOME MEASURES: Positive and negative predictive values at different PCT cut-off levels. RESULTS: The overall probability of an NS was doubled or more if PCT was >0.5 ng/ml. In very-low-birth-weight (VLBW) infants, a cut-off of >2.4 ng/ml gave a positive predictive value of NS near to 50% with a probability of a false-positive diagnosis of NS in about 10% of the patients. CONCLUSIONS: In VLBW neonates, a serum PCT value >2.4 ng/ml prompts early empirical antibiotic therapy, while in normal-birth-weight infants, a PCT value ≤2.4 ng/ml carries a low risk of missing an NS.

Reference values of blood cell counts in the first days of life.

The lack of updated neonatal reference values for hematological parameters impacts significantly with clinical management of both healthy and sick newborns. The present pilot study was thus aimed at assessing updated hematological Italian reference values in late preterm and term newborns. From January 2004 to December 2008 hematological laboratory tests were performed in 1175 newborns (820 healthy and 355 sick controls) between 33-41 weeks of gestation, during the first four days after birth. Hematological parameters were sorted for gender and gestational age and statistically analyzed. No gender-related differences were observed at different weeks of gestation and no significant differences were found when study population was sub-grouped for late preterm and term newborns. During the first 4 days of life erythrocytes and platelets remained stable whilst white blood cell counts and differentials were significantly modified. This study shares updated reference values for hematological parameters in the early phases after birth and offers additional support for improving the management of sick infants.

Determinants of nosocomial infection in 6 neonatal intensive care units: an Italian multicenter prospective cohort study.

BACKGROUND: Nosocomial infections are still a major cause of morbidity and mortality among neonates admitted to neonatal intensive care units (NICUs). OBJECTIVE: To describe the epidemiology of nosocomial infections in NICUs and to assess the risk of nosocomial infection related to the therapeutic procedures performed and to the clinical characteristics of the neonates at birth and at admission to the NICU, taking into account the time between the exposure and the onset of infection. DESIGN: A multicenter, prospective cohort study. PATIENTS AND SETTING: A total of 1,692 neonates admitted to 6 NICUs in Italy were observed and monitored for the development of nosocomial infection during their hospital stay. METHODS: Data were collected on the clinical characteristics of the neonates admitted to the NICUs, their therapeutic interventions and treatments, their infections, and their mortality rate. The cumulative probability of having at least 1 infection and the cumulative probability of having at least 1 infection or dying were estimated. The hazard ratio (HR) for the first infection and the HR for the first infection or death were also estimated. RESULTS: A total of 255 episodes of nosocomial infection were diagnosed in 217 neonates, yielding an incidence density of 6.9 episodes per 1,000 patient-days. The risk factors related to nosocomial infection in very-low-birth-weight neonates were receipt of continuous positive airway pressure (HR, 3.8 [95% confidence interval {CI}, 1.7-8.1]), a Clinical Risk Index for Babies score of 4 or greater (HR, 2.2 [95% CI, 1.4-3.4]), and a gestational age of less than 28 weeks (HR, 2.1 [95% CI, 1.2-3.8]). Among heavier neonates, the risk factors for nosocomial infection were receipt of parenteral nutrition (HR, 8.1 [95% CI, 3.2-20.5]) and presence of malformations (HR, 2.3 [95% CI, 1.5-3.5]). CONCLUSIONS: Patterns of risk factors for nosocomial infection differ between very-low-birth-weight neonates and heavier neonates. Therapeutic procedures appear to be strong determinants of nosocomial infection in both groups of neonates, after controlling for clinical characteristics.