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Cristina Dragomir,1 Roxana Popescu,2,3 Monica Alisa Jurca,4 Ruxandra Laza,5 Roxana Ivan Florian,6 Ion Dragomir,7 Romeo Negrea,8 Marius Craina,9 Cristina Adriana Dehelean10,11 1Doctoral School, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania; 2Department II – Microscopic Morphology, Discipline of Cellular and Molecular Biology, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania; 3ANAPATMOL Research Center, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania; 4County Emergency Clinical Hospital “Pius Brinzeu”, Timisoara, Romania; 5Department XIII, Discipline of Infectious Disease, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania; 6Dynata Company, Timisoara, Romania; 7Individual Family Medical Office, Ostroveni, Dolj, Romania; 8Department of Mathematics, Polytechnica University of Timisoara, Timisoara, Romania; 9Department XII - Obstetrics-Gynecology, Discipline of Obstetrics-Gynecology III, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania; 10Department of Toxicology and Drug Industry, Faculty of Pharmacy, University of Medicine and Pharmacy, Timisoara “Victor Babes”, Timișoara, Romania; 11FARMATOX Research Centre for Pharmaco-Toxicological Evaluation, University of Medicine and Pharmacy “Victor Babes”, Timisoara, RomaniaCorrespondence: Roxana Popescu; Cristina Dragomir, University of Medicine and Pharmacy “Victor Babes”, Eftimie Murgu Square, No. 2, Timisoara, 300041, Romania, Tel +40723649886 ; +40753036306, Email popescu.roxana@umft.ro; dr.cristinadragomir@yahoo.comPurpose: The purpose of this study is to identify the relationships between postpartum emotional manifestations and various neonatal variables, as well as variables within this category, in the context of hospitalization together after birth.Patients and Methods: Between 1 March 2020 and 1 September 2020, a cross-sectional research design was used including mother–child couples (112 mothers, 121 newborns - 13 twins/triplets).Results: Using a t-test for independent samples, we observed: a) the symptoms of depression were more severe in mothers of newborns hospitalized in neonatal intensive care units (NICUs) [t(110) = 4.334)], provided oxygen therapy [t(109.99) = 3.162], born prematurely [t(110) = 3.157], or with adjustment disorders [t(109) = − 2.947] (p < 0.01); b) a similar, for anxiety as a state [t(82.38) = 5.251], t(107.29) = 4.523, t(110) = 3.416, t(109) = − 3.268, p < 0.01], and as a trait was more common [t(80.79) = 4.501, t(108.790) = 4.669, t(109) = − 3.268, p < 0.001] compared to other mothers. Using Pearson’s test (p < 0.001), several very strong correlations were observed between neonatal variables, including number (no.) of days of hospitalization with birth weight (BW) (r = − 0.802), head circumference (HC) (r = − 0.822), and gestational age (GA) (r = − 0.800) and the mother’s postpartum anxiety as a state/trait (r = 0.770). Using Poisson regression, it was observed that anxiety as a state (Λ = 0.020, z = 4.029, p < 0.001) and as a trait (Λ = 0.800, z = 6.160, p < 0.001) stimulated the intensity of symptoms of postpartum depression (optimal models).Conclusion: Postpartum maternal psychological manifestations were associated with NICU hospitalization, pathology, and some neonatal therapies. We also noticed, that the duration of hospitalization, BW, HC, and GA, were correlated with maternal emotional disorders. Results will facilitate future optimization of birth management and postnatal care.Keywords: anxiety as a state, anxiety as a trait, attachment, postpartum depression symptoms, newborn at risk, prematurity

Ruxandra Laza,1,2 Cristina Dragomir,3 Virgil Filaret Musta,1,2 Voichita Elena Lazureanu,1,2 Narcisa Daniela Nicolescu,1,2 Adelina Raluca Marinescu,1– 3 Roxana Paczeyka,2 Tamara Mirela Porosnicu,2,3 Valerica Bica-Porfir,2 Sorina Maria Denisa Laitin,2,4 Ion Dragomir,5 Constantin Ilie6 ,† Luminita Mirela Baditoiu4,7 1Department XIII, Discipline of Infectious Diseases, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania; 2Clinical Hospital of Infectious Diseases and Pneumophtisiology “Doctor Victor Babes”, Timisoara, 300310, Romania; 3Doctoral School, University of Medicine and Pharmacy “Victor Babes”, Timisoara, 300041, Romania; 4Department XIII, Discipline of Epidemiology, University of Medicine and Pharmacy “Victor Babes”, Timisoara, 300041, Romania; 5Individual Family Medical Office, Ostroveni, Dolj, Romania; 6Department XII, Discipline of Neonatology and Childcare, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania; 7Multidisciplinary Research Centre on Antimicrobial Resistance, University of Medicine and Pharmacy “Victor Babes”, Timisoara, Romania†Constantin Ilie passed away on 27 January 2022Correspondence: Luminita Mirela Baditoiu, Cristina Dragomir Department XIII, Discipline of Epidemiology, Victor Babes University of Medicine and Pharmacy; Doctoral School, University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, Timisoara, 300041, Romania, Tel +40727746440 ; +40753036306, Email baditoiu.luminita@umft.ro; dr.cristinadragomir@yahoo.comPurpose: Romania is one of the European countries that has been hit the hardest by the severe acute respiratory syndrome caused by the new coronavirus SARS-CoV-2, with over 1.91 million reported cases and over 59,257 deaths. The aim of this study was to identify the main predictors of death in hospitalized patients.Patients and Methods: In the period from 1 March 2020 to 30 June 2021, an observational, retrospective, randomized, case-control study was conducted, which included a sample of 139 patients who died in hospital and another sample of 275 patients who had been discharged in an improved or healed condition. Confirmation of COVID-19 cases was performed by RT-PCR from nasopharyngeal and oropharyngeal exudates. Statistical data were analyzed by logistic regression, Cox regression and a comparison of survival curves by the log-rank (Mantel-Cox) test.Results: The most powerful logistic regression model identified the following independent predictors of death: history of coagulopathy HR = 30.73 [1.94– 487.09], p = 0.015; high percentage of neutrophils HR = 1.09 [1.01– 1.19], p = 0.027; and decreased blood-oxygenation HR = 53881.97 [1762.24– 1647489.44], p < 0.001. Cox regression identified the following factors that influenced the evolution of cases: history of coagulopathy HR = 2.44 [1.38– 4.35], p = 0.000; O2 saturation HR = 0.98 [0.96– 0.99], p = 0.043; serum creatinine HR = 1.23 [1.08– 1.39], p = 0.001; dyspnea on admission HR = 2.99 [1.42– 6.30], p = 0.004; hospitalization directly in the ICU HR = 3.803 [1.97– 7.33], p < 0.001; heart damage HR = 16.76 [1.49– 188.56], p = 0.022; and decreased blood-oxygenation HR = 35.12 [5.92– 208.19], p < 0.001.Conclusion: Knowledge of the predictors of death in hospitalized patients allows for the future optimization of triage and therapeutic case management for COVID-19.Keywords: complications, comorbidities, COVID-19, protection factors, risk factors, survival

The paraoxonase (PON) gene family in humans has three members, PON1, PON2, and PON3. Their physiological role(s) and natural substrates are uncertain. We developed a baculovirus-mediated expression system, suitable for all three human PONs, and optimized procedures for their purification. The recombinant PONs are glycosylated with high-mannose-type sugars, which are important for protein stability but are not essential for their enzymatic activities. Enzymatic characterization of the purified PONs has revealed them to be lactonases/lactonizing enzymes, with some overlapping substrates (e.g., aromatic lactones), but also to have distinctive substrate specificities. All three PONs metabolized very efficiently 5-hydroxy-eicosatetraenoic acid 1,5-lactone and 4-hydroxy-docosahexaenoic acid, which are products of both enzymatic and nonenzymatic oxidation of arachidonic acid and docosahexaenoic acid, respectively, and may represent the PONs' endogenous substrates. Organophosphates are hydrolyzed almost exclusively by PON1, whereas bulky drug substrates such as lovastatin and spironolactone are hydrolyzed only by PON3. Of special interest is the ability of the human PONs, especially PON2, to hydrolyze and thereby inactivate N-acyl-homoserine lactones, which are quorum-sensing signals of pathogenic bacteria.None of the recombinant PONs protected low density lipoprotein against copper-induced oxidation in vitro.

Purified serum paraoxonase (PON1) had been shown to attenuate the oxidation of LDL in vitro. We critically reevaluated the antioxidant properties of serum PON1 in the in vitro assays initiated with copper or the free radical generator 2,2′-azobis-2-amidinopropane hydrochloride (AAPH). The antioxidant activity of different purified PON1 preparations did not correlate with their arylesterase (AE), lactonase, or phospholipase A2 activities or with the amounts of detergent or protein. Dialysis of three of these preparations resulted in a 30–40% loss of their AE activities but in a complete loss of their antioxidant activities. We also followed the distribution of the antioxidant activity during human serum PON1 purification by two purification methods. The antioxidant activity of the anion-exchange chromatography fractions did not copurify with PON1 using either method and could largely be accounted for by the “antioxidant” activity of the detergent present.In conclusion, using the copper or AAPH in vitro assays, no PON1-mediated antioxidant activity was detected, suggesting that the removal of PON1 from its natural environment may impair its antioxidative activity and that this assay with highly purified PON1 may be an inappropriate method with which to study the antioxidative properties of the enzyme.

Paraoxonase-1 (PON1) is known to be associated with high density lipoproteins. We optimized buffer conditions to obtain quantitative recovery of PON1 (arylesterase) activity and analyzed the distribution of PON1 in mice using a combination of size-exclusion chromatography and ultracentrifugation. Size-exclusion chromatography of mouse serum separated the esterase activity into two peaks, one overlapping the high density lipoproteins and a second peak of lower molecular weight, consistent with serum carboxylesterase, which accounted for ∼20% of the total esterase activity of normal mouse serum. Using conditions for the quantitative recovery of arylesterase activity, we fractionated serum by ultracentrifugation into d < 1.21 g/ml, d < 1.25 g/ml, d > 1.21 g/ml, and d > 1.25 g/ml fractions. We observed that PON1 arylesterase activity and mass were isolated in the d < 1.21 g/ml fraction and that serum carboxylesterase was recovered in the d > 1.25 g/ml fraction. The significance of the confounding of PON1 arylesterase activity by serum carboxylesterase was demonstrated by studying mice challenged with a high-fat, high-cholate diet for 14 days. It was shown that all of the decrease in arylesterase activity in response to this diet is attributable to the HDL-associated arylesterase activity (PON1).We conclude that mouse PON1 is quantitatively associated with high density lipoproteins. The contribution of serum carboxylesterase to the total esterase activity significantly confounds the interpretation of total arylesterase activity in mouse serum.

In this paper presents protection methods against Electromagnetic straight of the radio waves in communication radio networks. Examples of personal protective equipment for monitoring EMF when working near transmitting devices. Personal Monitor. When an electric current flows through the human body, cells and tissues prevent the movement of charged particles. The value of the resistance depends on the type and condition of the cells, the value and frequency of the applied voltage and the duration. [ABSTRACT FROM AUTHOR]

This article compares the use of endoscopic ultrasound (EUS) and transjugular portal pressure measurements in assessing portal hypertension (PH). The study found that the measurements of PH by both methods were comparable, with a strong correlation between the values obtained. EUS-PPG measurement using a 22G needle was deemed accurate and safe. Further research is needed to determine the specific indications for EUS in patients requiring endoscopic assessment of portal hypertension. [Extracted from the article]

In this paper presents Electromagnetic Environment in cities. It noted that in the field of living hygiene, the concept of "risk" and safety of life is not sufficiently developed. This situation is preserved to this day, which creates real preconditions for the formation of unfavorable living conditions with damage to the health of the population. It was not until 1996 that the first hygiene standards for EMF levels were used when using consumer goods at home. [ABSTRACT FROM AUTHOR]

In this paper presents biological effect of the Electromagnetic field. The human body consists of cells, tissues, organs with different electrical characteristics. When an electric current flows through the human body, cells and tissues prevent the movement of charged particles. The value of the resistance depends on the type and condition of the cells, the value and frequency of the applied voltage and the duration. [ABSTRACT FROM AUTHOR]

Objective 1) To determine the pharmacokinetics of tramadol hydrochloride and its active metabolite, O-desmethyltramadol (M1), after administration through different routes in female and male C57Bl/6 mice; 2) to evaluate the stability of tramadol solutions; and 3) to identify a suitable dose regimen for prospective clinical analgesia in B6 mice. Study design Prospective, randomized, blinded, parallel design. Animals A total of 18 male and 18 female C57Bl/ 6 mice (20e30 g). Methods Mice were administered 25 mg kg-1 tramadol as a bolus [intravenously (IV), intraperitoneally (IP), subcutaneously (SQ), orally per gavage (OSObjective 1) To determine the pharmacokinetics of tramadol hydrochloride and its active metabolite, O-desmethyltramadol (M1), after administration through different routes in female and male C57Bl/6 mice; 2) to evaluate the stability of tramadol solutions; and 3) to identify a suitable dose regimen for prospective clinical analgesia in B6 mice. Study design Prospective, randomized, blinded, parallel design. Animals A total of 18 male and 18 female C57Bl/ 6 mice (20-30 g). Methods Mice were administered 25 mg kg-1 tramadol as a bolus [intravenously (IV), intraperitoneally (IP), subcutaneously (SQ), orally per gavage (OSgavage)] over 25 hours [orally in drinking water (OSwater) or Syrspend SF (OSSyrsp)]. Venous blood was sampled at six predetermined time points over 4 to 31 hours, depending on administration route, to determine tramadol and M1 plasma concentrations (liquid chromatography and tandem mass spectrometry detection). Pharmacokinetic parameters were described using a noncompartmental model. The stability of tramadol in water (acidified and untreated) and Syrspend SF (0.20 mg mL-1) at ambient conditions for 1 week was evaluated. Results After all administration routes, Cmax was >100 ng mL-1for tramadol and >40 ng mL-1for M1 (reported analgesic ranges in man) followed by short half-lives (2-6 hours). The mean tramadol plasma concentration after self-administration remained >100 ng mL-1throughout consumption time. M1 was found in the OSSyrs group only at 7 hours, whereas it was detectable in OSwater throughout administration. Tramadol had low oral bioavailability (26%). Short-lasting side effects were observed only after IV administration. Water and Syrspend SF solutions were stable for 1 week. Conclusions and clinical relevance 1) At the dose administered, high plasma concentrations of tramadol and M1 were obtained, with half-life depending on the administration route. 2) Plasma levels were stable over self-consumption time. 3) Solutions were stable for 1 week at ambient conditions.)] over 25 hours [orally in drinking water (OSwater) or Syrspend SF (OSSyrsp)]. Venous blood was sampled at six predetermined time points over 4 to 31 hours, depending on administration route, to determine tramadol and M1 plasma concentrations (liquid chromatography and tandem mass spectrometry detection). Pharmacokinetic parameters were described using a noncompartmental model. The stability of tramadol in water (acidified and untreated) and Syrspend SF (0.20 mg mL-1) at ambient conditions for 1 week was evaluated. Results After all administration routes, Cmax was >100 ng mL-1for tramadol and >40 ng mL-1for M1 (reported analgesic ranges in man) followed by short half-lives (2e6 hours). The mean tramadol plasma concentration after self-administration remained >100 ng mL-1throughout consumption time. M1 was found in the OSSyrs group only at 7 hours, whereas it was detectable in OSwater throughout administration. Tramadol had low oral bioavailability (26%). Short-lasting side effects were observed only after IV administration. Water and Syrspend SF solutions were stable for 1 week. Conclusions and clinical relevance 1) At the dose administered, high plasma concentrations of tramadol and M1 were obtained, with half-life depending on the administration route. 2) Plasma levels were stable over self-consumption time. 3) Solutions were stable for 1 week at ambient conditions. [ABSTRACT FROM AUTHOR]

Like other nitric-oxide synthase (NOS) enzymes, neuronal NOS (nNOS) turnover and activity are regulated by the ubiquitous protein chaperone hsp90. We have shown previously that nNOS expressed in Sf9 cells where endogenous heine levels are low is activated from the apo- to the holo-enzyme by addition of exogenous heine to the culture medium, and this activation is inhibited by radicicol, a specific inhibitor of hsp90 (Billecke, S. S., Bender, A. T., Kanelakis, K. C., Murphy, P. J. M., Lowe, E. R., Kamada, Y., Pratt, W. B., and Osawa, Y. (2002) J. Biol. Chem. 278, 1546515468). In this work, we examine heme binding by aponNOS to form the active enzyme in a cell-free system. We show that cytosol from Sf9 cells facilitates heme-dependent apo-nNOS activation by promoting functional heme insertion into the enzyme. Sf9 cytosol also converts the glucocorticoid receptor (GR) to a state where the hydrophobic ligand binding cleft is open to access by steroid. Both cell-free heme activation of purified nNOS and actiration of steroid binding activity of the immunopurified GR are inhibited by radicicol treatment of Sf9 cells prior to cytosol preparation, and addition of purified hsp90 to cytosol partially overcomes this inhibition. Although there is an hsp90-dependent machinery in Sf9 cytosol that facilitates heine binding by apo-nNOS, it is clearly different from the machinery that facilitates steroid binding by the GR. hsp90 regulation of apo-nNOS heme activation is very dynamic and requires higher concentrations of radicicol for its inhibition, whereas GR steroid binding is determined by assembly of stable GR·hsp90 heterocomplexes that are formed by a purified five-chaperone machinery that does not activate apo-nNOS. [ABSTRACT FROM AUTHOR]

Abstract: Serum paraoxonase (PON1) is well recognized for its ability to hydrolyze arylesters, toxic oxon metabolites of organophosphate insecticides and nerve agents. PON1 is a member of gene family including also PON2 and PON3; however, the later two enzymes have very limited arylesterase and practically no organophosphatase activity. We have established that all three PONs are lactonases/lactonyzing enzymes with overlapping, but also distinct substrate specificity. Dihydrocoumarin (DHC), long chain fatty acid lactones and acylhomoserine lactones (AHLs) are hydrolyzed by all three PONs and likely represent their natural substrates. The 3D structure of PON1 is a six-bladed β-propeller containing two Ca2+ ions necessary for the enzyme stability and enzymatic activity. Senescence marker protein (SMP30), another putative six-bladed β-propeller, hydrolyzes DFP, sarin and soman in the presence of Mg2+ or Mn2+. More recently, SMP30 was characterized as a gluconolactonase with a role in vitamin C metabolism. Bacterial phosphotriesterases (PTEs) are members of the amidohydrolase superfamily and differ in their structure from the eukaryotic organophosphatases; PTEs are (β/α)8 barrels with an active site containing two transition metal ions such as Co2+, Mn2+ or Zn2+. PTE from Pseudomonas diminuta hydrolyzes paraoxon extremely efficiently; this enzyme was shown to hydrolyze also DHC and other lactones. At least 3 more bacterial lactonases, dubbed PTE-like lactonases (or PLL), have been identified to possess both lactonase and organophosphatase activities. Lactones are natural compounds, many of them with high biological activity, while organophosphates are human-made chemicals introduced in the 20th century. Thus, it is plausible that lactonase is the primary activity for which the enzymes discussed here evolved for, while the organophosphatase activity arose as a promiscuous activity during their evolution. Laboratory (directed) evolution studies provided mechanisms for their catalytic versatility and demonstrated experimentally the evolvability of promiscuous enzyme functions. [Copyright &y& Elsevier]

Abstract: Mammalian paraoxonases (PONs 1, 2 and 3) are a highly conserved family of esterases, with uncertain physiological functions and natural substrates. Here we characterize the ability of purified recombinant human PONs to hydrolyze estrogen esters, a class of compounds previously not known to be PON substrates. PONs hydrolyzed estrogen mono- and diesters at position 3 of the steroid A-ring. Diesters were better substrates for the PONs and were very efficiently hydrolyzed, particularly by PON3. Esters at position 17 were not cleaved by the PONs unless an adjacent double bound was present. Purified human serum butyryl cholinesterase also hydrolyzed estrogen esters, however it preferably hydrolyzed the mono-esters. The ability of the PONs’ to effectively hydrolyze a variety of estrogen esters provides further insight into the structure of their active sites and suggests that natural compounds with aromatic ester groups might be relevant substrates for the PONs. [Copyright &y& Elsevier]

Portal hypertension-related complications increase mortality in patients, irrespective of its etiology. Classically, endoscopic ultrasound (EUS) was used to assess the portal venous system and collaterals, considering size and hemodynamic parameters, which correlate with portal hypertension (PH) and related complications. Furthermore, therapeutic EUS guides treatment interventions, such as embolization of the gastric varices through coil placement and tissue adhesive injection, yielding encouraging clinical results. Recently, the direct measurement of portal pressure, emerging as an alternative to hepatic venous pressure gradient, has shown promise, and further research in this area is anticipated. In this review, we aimed to provide a detailed description of various possibilities for diagnosing vascular anatomy and hemodynamics in PH and actual knowledge on the EUS usefulness for PH vessel-related complications. Also, future promises for this field of endo-hepatology are discussed., Competing Interests: None declared., (© The Author(s) 2024. Published by Oxford University Press and Sixth Affiliated Hospital of Sun Yat-sen University.)

The exploration of single-strand DNA-binding protein (SSB)-ssDNA interactions and their crucial roles in essential biological processes lagged behind other types of protein-nucleic acid interactions, such as protein-dsDNA and protein-RNA interactions. The ssDNA binding protein gene product 32 (gp32) of the T4 bacteriophage is a central integrating component of the replication complex that must continuously bind to and unbind from transiently exposed template strands during the DNA synthesis. To gain deeper insights into the electrostatic conditions influencing the stability of the ssDNA-gp32 molecular complex, like the salt concentration or some metal ions proven to specifically bind to gp32, we employed a method that performs rapid measurements of the DNA-protein stability using an α-Hemolysin (α-HL) protein nanopore. We indirectly probed the stability of a protein-nucleic acid complex by monitoring the dissociation process between the gp32 protein and the ssDNA molecular complex in single-molecular electrophysiology experiments, but also through fluorescence spectroscopy techniques. We have shown that the complex is more stable in 0.5 M KCl solution than in 2 M KCl solution and that the presence of Zn 2+ ions further increases this stability for any salt used in the present study. This method can be applied to other nucleic acid-protein molecular complexes, as well as for an accurate determination of the drug-protein carrier stability., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Background and objectives: The postpartum maternal physical and psychological state played a fundamental role in the mother−child relationship at the beginning of the COVID-19 pandemic. The aim of the study is to analyze the influence of maternal psychological manifestations on the mother−child couple through three objectives (briefly expressed): (I) Determination of the main acute and chronic conditions of newborns/infants. (II) Verification of the hypothesis of the existence of a link between the following neonatal variables: gestational age, birth weight, number of days of hospitalization, and specific neonatal therapies (oxygen, surfactant, and blood products’ transfusion). (III) Verification of the influence of postpartum maternal psychological status on the mother−child couple through three hypotheses. Materials and methods: This cross-sectional study was conducted in two hospitals in Timișoara, Romania, between 1 March and 1 September 2020, and included 165 mothers and their 175 newborns. Mothers answered the Edinburgh Postnatal Depression Scale, Spielberger’s Inventory of State-Trait Anxiety, and the Collins and Read Revised Adult Attachment Scale. Results: (I) The acute and chronic pathology of the infants in the study group was polymorphic. (II) Large correlations were identified between the following infant variables: gestational age with birth weight, and number of hospitalization days with birth weight, gestational age, and use of blood product transfusion (all p < 0.001). (III) (1) State anxiety was the only significant predictor of number of hospitalization days (p = 0.037), number of acute disorders (p = 0.028), and number of infant chronic diseases (p = 0.037). (2) Maternal depressive symptoms were the only predictor of postpartum maternal attachment (p = 0.018). (3) Depressive symptoms, state, and trait anxiety were non-significant in all models studied (all p > 0.05). Conclusions: Postpartum maternal physical and psychological state plays a fundamental role on the mother−child relationship in the new social and complex family conditions.

Real-time monitoring, simple operation, and cheaper methods for detecting immunological proteins hold the potential for a solid influence on proteomics and human biology, as they can promote the onset of timely diagnoses and adequate treatment protocols. In this work we present an exploratory study suggesting the applicability of resistive-pulse sensing technology in conjunction with the α-hemolysin (α-HL) protein nanopore, for the detection of the chronic hepatitis B virus (HBV) e-antigen (HBeAg). In this approach, the recognition between HBeAg and a purified monoclonal hepatitis B e antibody (Ab(HBeAg)) was detected via transient ionic current spikes generated by partial occlusions of the α-HL nanopore by protein aggregates electrophoretically driven toward the nanopore's vestibule entrance. Despite the steric hindrance precluding antigen, antibody, or antigen-antibody complex capture inside the nanopore, their stochastic bumping with the nanopore generated clear transient blockade events. The subsequent analysis suggested the detection of protein subpopulations in solution, rendering the approach a potentially valuable label-free platform for the sensitive, submicromolar-scale screening of HBeAg targets.

Real-time and easy-to-use detection of nucleic acids is crucial for many applications, including medical diagnostics, genetic screening, forensic science, or monitoring the onset and progression of various diseases. Herein, an exploratory single-molecule approach for multiplexed discrimination among similar-sized single-stranded DNAs (ssDNA) is presented. The underlying strategy combined (i) a method based on length-variable, short arginine (poly-Arg) tags appended to peptide nucleic acid (PNA) probes, designed to hybridize with selected regions from complementary ssDNA targets (cDNA) in solution and (ii) formation and subsequent detection with the α-hemolysin nanopore of (poly-Arg)-PNA-cDNA duplexes containing two overhangs associated with the poly-Arg tail and the non-hybridized segment from ssDNA. We discovered that the length-variable poly-Arg tail marked distinctly the molecular processes associated with the nanopore-mediated duplexes capture, trapping and unzipping. This enabled the detection of ssDNA targets via the signatures of (poly-Arg)-PNA-cDNA blockade events, rendered most efficient from the β-barrel entrance of the nanopore, and scaled proportional in efficacy with a larger poly-Arg moiety. We illustrate the approach by sensing synthetic ssDNAs designed to emulate fragments from two regions of SARS-CoV-2 nucleocapsid phosphoprotein N-gene.

Sporadic cancer develops from the accrual of somatic mutations. Out of all small-scale somatic aberrations in coding regions, 95% are base substitutions, with 90% being missense mutations. While multiple studies focused on the importance of this mutation type, a machine learning method based on the number of protein-protein interactions (PPIs) has not been fully explored. This study aims to develop an improved computational method for driver identification, validation and evaluation (DRIVE), which is compared to other methods for assessing its performance. DRIVE aims at distinguishing between driver and passenger mutations using a feature-based learning approach comprising two levels of biological classification for a pan-cancer assessment of somatic mutations. Gene-level features include the maximum number of protein-protein interactions, the biological process and the type of post-translational modifications (PTMs) while mutation-level features are based on pathogenicity scores. Multiple supervised classification algorithms were trained on Genomics Evidence Neoplasia Information Exchange (GENIE) project data and then tested on an independent dataset from The Cancer Genome Atlas (TCGA) study. Finally, the most powerful classifier using DRIVE was evaluated on a benchmark dataset, which showed a better overall performance compared to other state-of-the-art methodologies, however, considerable care must be taken due to the reduced size of the dataset. DRIVE outlines the outstanding potential that multiple levels of a feature-based learning model will play in the future of oncology-based precision medicine.

Cell-penetrating peptides (CPPs) have the property to cross the plasma membrane and enhance its permeability. CPPs were successfully used to deliver numerous cargoes such as drugs, proteins, nucleic acids, imaging and radiotherapeutic agents, gold and magnetic nanoparticles, or liposomes inside cells. Although CPPs were intensively investigated over the past 20 years, the exact molecular mechanisms of translocation across membranes are still controversial and vary from passive to active mechanisms. LyP-1 is a cyclic 9-amino-acids homing peptide that specifically binds to p32 receptors overexpressed in tumor cells. tLyP-1 peptide is the linear truncated form of LyP-1 and recognizes neuropilin (NRP) receptors expressed in glioma tumor tissue. Here, we investigate the interaction of the cyclic LyP-1 peptide and linear truncated tLyP-1 peptide with model plasma membrane in order to understand their passive, energy-independent mechanism of uptake. The experiments reveal that internalization of tLyP-1 peptides depends on membrane lipid composition. Inclusion of negatively charged phosphatidylserine (PS) or cone-shaped phosphatidylethanolamine (PE) lipids in the composition of giant unilamellar vesicles facilitates the membrane adsorption and direct penetration but without inducing pore formation in membranes. In contrast, cyclic LyP-1 peptide mostly accumulates on the membrane, with very low internalization, regardless of the lipid composition. Thus, the linear tLyP-1 peptide has enhanced penetrating properties compared with the cyclic LyP-1 peptide. Development of a mutant peptide containing higher number of arginine amino acids and preserving the homing properties of tLyP-1 may be a solution for new permeable peptides that facilitate the internalization in cells and further the endosomal escape as well., (© 2018 European Peptide Society and John Wiley & Sons, Ltd.)

TAR DNA-binding protein 43 (TDP-43) is normally a nuclear RNA-binding protein that exhibits a range of functions including regulation of alternative splicing, RNA trafficking, and RNA stability. However, in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), TDP-43 is abnormally phosphorylated, ubiquitinated, and cleaved, and is mislocalized to the cytoplasm where it forms distinctive aggregates. We previously developed a mouse model expressing human TDP-43 with a mutation in its nuclear localization signal (ΔNLS-hTDP-43) so that the protein preferentially localizes to the cytoplasm. These mice did not exhibit a significant number of cytoplasmic aggregates, but did display dramatic changes in gene expression as measured by microarray, suggesting that cytoplasmic TDP-43 may be associated with a toxic gain-of-function. Here, we analyze new RNA-sequencing data from the ΔNLS-hTDP-43 mouse model, together with published RNA-sequencing data obtained previously from TDP-43 antisense oligonucleotide (ASO) knockdown mice to investigate further the dysregulation of gene expression in the ΔNLS model. This analysis reveals that the transcriptomic effects of the overexpression of the ΔNLS-hTDP-43 transgene are likely due to a gain of cytoplasmic function. Moreover, cytoplasmic TDP-43 expression alters transcripts that regulate chromatin assembly, the nucleolus, lysosomal function, and histone 3' untranslated region (UTR) processing. These transcriptomic alterations correlate with observed histologic abnormalities in heterochromatin structure and nuclear size in transgenic mouse and human brains.

RNA is often altered post-transcriptionally by the covalent modification of particular nucleotides; these modifications are known to modulate the structure and activity of their host RNAs. The recent discovery that an RNA methyl-6 adenosine demethylase (FTO) is a risk gene in obesity has brought to light the significance of RNA modifications to human biology. These noncanonical nucleotides, when converted to cDNA in the course of RNA sequencing, can produce sequence patterns that are distinguishable from simple base-calling errors. To determine whether these modifications can be detected in RNA sequencing data, we developed a method that can not only locate these modifications transcriptome-wide with single nucleotide resolution, but can also differentiate between different classes of modifications. Using small RNA-seq data we were able to detect 92% of all known human tRNA modification sites that are predicted to affect RT activity. We also found that different modifications produce distinct patterns of cDNA sequence, allowing us to differentiate between two classes of adenosine and two classes of guanine modifications with 98% and 79% accuracy, respectively. To show the robustness of this method to sample preparation and sequencing methods, as well as to organismal diversity, we applied it to a publicly available yeast data set and achieved similar levels of accuracy. We also experimentally validated two novel and one known 3-methylcytosine (3mC) sites predicted by HAMR in human tRNAs. Researchers can now use our method to identify and characterize RNA modifications using only RNA-seq data, both retrospectively and when asking questions specifically about modified RNA.

Persistent infection of the mouse central nervous system (CNS) with mouse hepatitis virus (MHV) induces a demyelinating disease pathologically similar to multiple sclerosis and is therefore used as a model system. There is little information regarding the host factors that correlate with and contribute to MHV-induced demyelination. Here, we detail the genes and pathways associated with MHV-induced demyelinating disease in the spinal cord. High-throughput sequencing of the host transcriptome revealed that demyelination is accompanied by numerous transcriptional changes indicative of immune infiltration as well as changes in the cytokine milieu and lipid metabolism. We found evidence that a Th1-biased cytokine/chemokine response and eicosanoid-derived inflammation accompany persistent MHV infection and that antigen presentation is ongoing. Interestingly, increased expression of genes involved in lipid transport, processing, and catabolism, including some with known roles in neurodegenerative diseases, coincided with demyelination. Lastly, expression of several genes involved in osteoclast or bone-resident macrophage function, most notably TREM2 and DAP12, was upregulated in persistently infected mouse spinal cord. This study highlights the complexity of the host antiviral response, which accompany MHV-induced demyelination, and further supports previous findings that MHV-induced demyelination is immune-mediated. Interestingly, these data suggest a parallel between bone reabsorption by osteoclasts and myelin debris clearance by microglia in the bone and the CNS, respectively. To our knowledge, this is the first report of using an RNA-seq approach to study the host CNS response to persistent viral infection.

The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA]) and unpaired (single-stranded RNA [ssRNA]) components of the Drosophila melanogaster and Caenorhabditis elegans transcriptomes, which allows us to identify conserved features of RNA secondary structure in metazoans. From this analysis, we find that ssRNAs and dsRNAs are significantly correlated with specific epigenetic modifications. Additionally, we find key structural patterns across protein-coding transcripts that indicate that RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in animals. Finally, we identify and characterize 546 mRNAs whose folding pattern is significantly correlated between these metazoans, suggesting that their structure has some function. Overall, our findings provide a global assessment of RNA folding in animals., (Copyright © 2012 The Authors. Published by Elsevier Inc. All rights reserved.)

Mammalian paraoxonases (PONs) are a unique, highly conserved family of calcium-dependent esterases consisting of PON1, PON2, and PON3. The PONs can hydrolyze the lactone ring of a range of N-acyl-L: -homoserine lactone (AHL) quorum sensing signaling molecules, rendering them inactive. This chapter describes a method that utilizes high-performance liquid chromatography analysis with UV detection for determining the rate of AHL hydrolysis in cell lysates, tissue homogenates, serum, and with purified proteins. Also described are the techniques used to prepare cell culture lysates and tissue homogenates for analysis and the use of class-specific enzyme inhibitors to determine the contribution of PONs to AHL hydrolysis in the samples.

The functional structure of all biologically active molecules is dependent on intra- and inter-molecular interactions. This is especially evident for RNA molecules whose functionality, maturation, and regulation require formation of correct secondary structure through encoded base-pairing interactions. Unfortunately, intra- and inter-molecular base-pairing information is lacking for most RNAs. Here, we marry classical nuclease-based structure mapping techniques with high-throughput sequencing technology to interrogate all base-paired RNA in Arabidopsis thaliana and identify ∼200 new small (sm)RNA-producing substrates of RNA-DEPENDENT RNA POLYMERASE6. Our comprehensive analysis of paired RNAs reveals conserved functionality within introns and both 5' and 3' untranslated regions (UTRs) of mRNAs, as well as a novel population of functional RNAs, many of which are the precursors of smRNAs. Finally, we identify intra-molecular base-pairing interactions to produce a genome-wide collection of RNA secondary structure models. Although our methodology reveals the pairing status of RNA molecules in the absence of cellular proteins, previous studies have demonstrated that structural information obtained for RNAs in solution accurately reflects their structure in ribonucleoprotein complexes. Furthermore, our identification of RNA-DEPENDENT RNA POLYMERASE6 substrates and conserved functional RNA domains within introns and both 5' and 3' untranslated regions (UTRs) of mRNAs using this approach strongly suggests that RNA molecules are correctly folded into their secondary structure in solution. Overall, our findings highlight the importance of base-paired RNAs in eukaryotes and present an approach that should be widely applicable for the analysis of this key structural feature of RNA., Competing Interests: The authors have declared that no competing interests exist.

The pathogenic bacterium Pseudomonas aeruginosa causes serious infections in immunocompromised patients. N-(3-oxododecanoyl)-L-homoserine lactone (3OC12-HSL) is a key component of P. aeruginosa's quorum-sensing system and regulates the expression of many virulence factors. 3OC12-HSL was previously shown to be hydrolytically inactivated by the paraoxonase (PON) family of calcium-dependent esterases, consisting of PON1, PON2, and PON3. Here we determined the specific activities of purified human PONs for 3OC12-HSL hydrolysis, including the common PON1 polymorphic forms, and found they were in the following order: PON2 >> PON1(192R) > PON1(192Q) > PON3. PON2 exhibited a high specific activity of 7.6 +/- 0.4 micromols/min/mg at 10 microM 3OC12-HSL, making it the best PON2 substrate identified to date. By use of class-specific inhibitors, approximately 85 and 95% of the 3OC12-HSL lactonase activity were attributable to PON1 in mouse and human sera, respectively. In mouse liver homogenates, the activity was metal dependent, with magnesium- and manganese-dependent lactonase activities comprising 10 to 15% of the calcium-dependent activity. In mouse lung homogenates, all of the activity was calcium dependent. The calcium-dependent activities were irreversibly inhibited by extended EDTA treatment, implicating PONs as the major enzymes inactivating 3OC12-HSL. In human HepG2 and EA.hy 926 cell lysates, the 3OC12-HSL lactonase activity closely paralleled the PON2 protein levels after PON2 knockdown by small interfering RNA treatment of the cells. These findings suggest that PONs, particularly PON2, could be an important mechanism by which 3OC12-HSL is inactivated in mammals.

The charge transfer (CT) band at 695 nm in the spectrum of ferri-cytochrome c is highly asymmetric, indicating conformational heterogeneity due to the coexistence of different conformational substates. We have measured the respective band profile of horse heart ferri-cytochrome c as a function of temperature between 283 K (10 degrees C) and 333 K (60 degrees C) and found that the well-known decrease of the absorptivity is wavenumber-dependent and exhibits a biphasic behavior. This indicates that the underlying conformational substates differ in their thermodynamic stability with respect to the structural changes associated with the disappearance of the 695 nm band, which eventually (at high temperatures) involves the replacement of M80 by a nearby lysine residue. Our data further indicates that the thermal unfolding process involves two structurally different intermediate states.

We have measured the electronic circular dichroism (ECD) of the ferri- and ferro-states of several natural cytochrome c derivatives (horse heart, chicken, bovine, and yeast) and the Y67F mutant of yeast in the region between 300 and 750 nm. Thus, we recorded the ECD of the B- and Q-band region as well as the charge-transfer band at approximately 695 nm. The B-band region of the ferri-state displays a nearly symmetric couplet at the B0-position that overlaps with a couplet 790 cm-1 higher in energy, which we assigned to a vibronic side-band transition. For the ferro-state, the couplet is greatly reduced, but still detectable. The B-band region is dominated by a positive Cotton effect at energies lower than B0 that is attributed to a magnetically allowed iron-->heme charge-transfer transition as earlier observed for nitrosyl myoglobin and hemoglobin. The Q-band region of the ferri-state is poorly resolved, but displays a pronounced positive signal at higher wavenumbers. This must result from a magnetically allowed transition, possibly from the methionine ligand to the dxy-hole of Fe3+. For the ferro-state, the spectra resolve the vibronic structure of the Qv-band. A more detailed spectral analysis reveals that the positively biased spectrum can be understood as a superposition of asymmetric couplets of split Q0 and Qv-states. Substantial qualitative and quantitative differences between the respective B-state and Q-state ECD spectra of yeast and horse heart cytochrome c can clearly be attributed to the reduced band splitting in the former, which results from a less heterogeneous internal electric field. Finally, we investigated the charge-transfer band at 695 nm in the ferri-state spectrum and found that it is composed of at least three bands, which are assignable to different taxonomic substates. The respective subbands differ somewhat with respect to their Kuhn anisotropy ratio and their intensity ratios are different for horse and yeast cytochrome c. Our data therefore suggests different substate populations for these proteins, which is most likely assignable to a structural heterogeneity of the distal Fe-M80 coordination of the heme chromophore.

We measured the temperature-dependent electronic circular dichroism (ECD) spectra of AX, XA, and XG dipeptides in D2O. The spectra of all XA and AX peptides indicate a substantial population of the polyproline II (PPII) conformation, while the ECD spectra of LG, KG, PG, and AG were found to be quantitatively different from the alanine-based dipeptides. Additional UV absorption data indicate that the ECD spectra of the XG peptides stem from electronic coupling between the peptide and the C-terminal group, and that spectral differences reflect different orientations of the latter. We also measured the 1H NMR spectra of the investigated dipeptides to determine the 3JHalphaNH coupling constants for the C-terminal residue. The observed temperature dependence of the ECD spectra and the respective room-temperature 3JHalphaNH coupling constants were analyzed by a two-state model encompassing PPII and a beta-like conformation. The PPII propensity of alanine in the XA series is only slightly modulated by the N-terminal side chain, and is larger than 50%. As compared to AA, XA peptides containing L, P, S, K V, E, T, and I all cause a relative stabilization of the extended beta-strand conformation. The PPII fractions of XA peptides varied between 0.64 for AA and 0.58 for DA, whereas the PPII fractions of AX peptides were much lower. From the investigated AX peptides, only AL and AQ showed the expected PPII propensity. We found that AT, AI, and AV clearly prefer an extended beta-strand conformation. A quantitative comparison of AA, AAA, and AAAA revealed a hierarchy AAAA > AAA approximately AA for the PPII population, in agreement with predictions from MD calculations and results from Raman optical activity studies (McColl et al. J. Am. Chem. Soc. 2004, 126, 5076).

The paraoxonase (PON) gene family in humans has three members, PON1, PON2, and PON3. Their physiological role(s) and natural substrates are uncertain. We developed a baculovirus-mediated expression system, suitable for all three human PONs, and optimized procedures for their purification. The recombinant PONs are glycosylated with high-mannose-type sugars, which are important for protein stability but are not essential for their enzymatic activities. Enzymatic characterization of the purified PONs has revealed them to be lactonases/lactonizing enzymes, with some overlapping substrates (e.g., aromatic lactones), but also to have distinctive substrate specificities. All three PONs metabolized very efficiently 5-hydroxy-eicosatetraenoic acid 1,5-lactone and 4-hydroxy-docosahexaenoic acid, which are products of both enzymatic and nonenzymatic oxidation of arachidonic acid and docosahexaenoic acid, respectively, and may represent the PONs' endogenous substrates. Organophosphates are hydrolyzed almost exclusively by PON1, whereas bulky drug substrates such as lovastatin and spironolactone are hydrolyzed only by PON3. Of special interest is the ability of the human PONs, especially PON2, to hydrolyze and thereby inactivate N-acyl-homoserine lactones, which are quorum-sensing signals of pathogenic bacteria. None of the recombinant PONs protected low density lipoprotein against copper-induced oxidation in vitro.