Multiplex Digital PCR-Based Development and discussion of the Detection of Genetic Association Between Staphylococcus aureus and mecA.

Methicillin-resistant Staphylococcus aureus (MRSA) is a predominant nosocomial infection-causing bacteria. The aim of this study was to develop a novel single-bacteria multiplex digital PCR assays (SMD-PCR), which is capable of simultaneously detecting and discriminating Methicillin-sensitive Staphylococcus aureus (MSSA) and MRSA. This protocol employed TaqMan probes to detect SAOUHSC_00106 and mecA genes, with the latter being linked to methicillin resistance. A total of 72 samples from various specimen types were evaluated. The accuracy rates for the sputum samples, pus samples, swab samples, ear secretion samples, and catheter samples were 94.44%, 100%, 92%, 100%, and 100%, respectively. Our results showed that the clinical practicability of SMD-PCR has applicability to the rapid detection of MRSA without DNA extraction or bacterial culture, and can be utilized for the rapid detection of Staphylococcus aureus and the timely identification of MRSA in clinical samples, thereby providing an advanced platform for the rapid diagnosis of clinical MRSA infection.

End-of-life care for cancer patients with pre-existing severe mental disorders-a systematic review.

BACKGROUND: Cancer patients with pre-existing severe mental disorders (SMDs) less frequently receive guideline recommended cancer treatment and have a higher cancer mortality. However, knowledge is needed concerning end-of-life care in this patient group. The aim of this systematic review was to provide an overview of the literature concerning end-of-life care in cancer patients with pre-existing SMD. METHODS: A systematic search was conducted in the following databases: PubMed, Embase and Science Direct and all results were downloaded to Endnote on 1st of September 2023. The review was registered on International Prospective Register of Systematic Reviews (PROSPERO) (ID: CRD42023468571). The quality of the studies was assessed according to the Newcastle-Ottawa Scale. RESULTS: Ten studies fulfilling the inclusion criteria were included. There was a recurring pattern indicating a difference between the end-of-life care received by cancer patients with SMD, compared to those without. Cancer patients with pre-existing SMD received more palliative end-of-life care but less high-intensive-end-of-life (HIEOL) care, e.g., less hospitalisations and chemotherapy at the end of life, and died less frequently at hospital. CONCLUSIONS: The study indicates that patients with pre-existing SMD and cancer more often received palliative end-of-life care and less HIEOL care compared to controls. Further research regarding the difference in end-of-life care is lacking, including the consequences of less intense HIEOL care for this patient group. Thus, further studies are needed to identify reasons for less intense HIEOL among cancer patients with pre-existing SMD.

Unveiling dissociation mechanisms and binding patterns in the UHRF1-DPPA3 complex via multi-replica molecular dynamics simulations.

CONTEXT: Ubiquitin-like with PHD and RING finger domain containing protein 1 (UHRF1) is responsible for preserving the stability of genomic methylation through the recruitment of DNA methyltransferase 1 (DNMT1). However, the interaction between Developmental pluripotency associated 3 (DPPA3) and the pre-PHD-PHD (PPHD) domain of UHRF1 hinders the nuclear localization of UHRF1. This disruption has implications for potential cancer treatment strategies. Drugs that mimic the binding pattern between DPPA3 and PPHD could offer a promising approach to cancer treatment. Our study reveals that DPPA3 undergoes dissociation from the C-terminal through three different modes of helix unfolding. Furthermore, we have identified key residue pairs involved in this dissociation process and potential drug-targeting residues. These findings offer valuable insights into the dissociation mechanism of DPPA3 from PPHD and have the potential to inform the design of novel drugs targeting UHRF1 for cancer therapy. METHODS: To comprehend the dissociation process and binding patterns of PPHD-DPPA3, we employed enhanced sampling techniques, including steered molecular dynamics (SMD) and conventional molecular dynamics (cMD). Additionally, we utilized self-organizing maps (SOM) and time-resolved force distribution analysis (TRFDA) methodologies. The Gromacs software was used for performing molecular dynamics simulations, and the AMBER FF14SB force field was applied to the protein.

Molecular Mechanism of Interaction between DNA Aptamer and Receptor-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus 2 Variants Revealed by Steered Molecular Dynamics Simulations.

The ongoing SARS-CoV-2 pandemic has underscored the urgent need for versatile and rapidly deployable antiviral strategies. While vaccines have been pivotal in controlling the spread of the virus, the emergence of new variants continues to pose significant challenges to global health. Here, our study focuses on a novel approach to antiviral therapy using DNA aptamers, short oligonucleotides with high specificity and affinity for their targets, as potential inhibitors against the spike protein of SARS-CoV-2 variants Omicron and JN.1. Our research utilizes steered molecular dynamics (SMD) simulations to elucidate the binding mechanisms of a specifically designed DNA aptamer, AM032-4, to the receptor-binding domain (RBD) of the aforementioned variants. The simulations reveal detailed molecular insights into the aptamer-RBD interaction, demonstrating the aptamer's potential to maintain effective binding in the face of rapid viral evolution. Our work not only demonstrates the dynamic interaction between aptamer-RBD for possible antiviral therapy but also introduces a computational method to study aptamer-protein interactions.

Increased LACTB2 Expression Regulates Oxidative Phosphorylation and mTORC1 Signaling of Colorectal Cancer.

This study aimed to investigate the mechanisms of LACTB2 in colorectal cancer (CRC). Microarrays and sequencing data of CRC were acquired from UCSC Xena, GTEx, Gene Expression Omnibus, and TCGA. Pooled analysis of the mRNA expression of LACTB2 in CRC was performed using Stata software. The protein expression of LACTB2 in CRC tissues was evaluated by immunohistochemistry. The relationship between immune cell infiltration and LACTB2 expression was investigated using CIBERSORT. The potential signaling pathways and biological mechanisms of LACTB2 were explored using GSEA, KEGG, and GO. Subsequently, further screening of small molecular compounds with potential therapeutic effects on CRC was conducted through the HERB database, followed by molecular docking studies of these compounds with the LACTB2 protein. The integration and analysis of expression data obtained from 2294 CRC samples and 1286 noncancerous colorectal samples showed that LACTB2 was highly expressed in CRC. Immunohistochemistry performed on in-house tissue samples confirmed that LACTB2 protein expression was upregulated in CRC. CIBERSORT revealed lower B cell infiltration levels in the high LACTB2 expression group than in the low expression group. GO, KEGG, and GSEA analyses showed that LACTB2 expression and genes positively correlating with it were mainly related to DNA synthesis and repair, mitochondrial translational elongation and translational termination, phosphorylation, and mTORC1 signaling. Finally, molecular docking simulations confirmed the ability of quercitin to target and bind to LACTB2. This is the first study to demonstrate that LACTB2 is upregulated in CRC. LACTB2 promotes colorectal tumorigenesis and tumor progression.

Developing Dynamic Structure-Based Pharmacophore and ML-Trained QSAR Models for the Discovery of Novel Resistance-Free RET Tyrosine Kinase Inhibitors Through Extensive MD Trajectories and NRI Analysis.

Activation of RET tyrosine kinase plays a critical role in the pathogenesis of various cancers, including non-small cell lung cancer, papillary thyroid cancers, multiple endocrine neoplasia type 2A and 2B (MEN2A, MEN2B), and familial medullary thyroid cancer. Gene fusions and point mutations in the RET proto-oncogene result in constitutive activation of RET signaling pathways. Consequently, developing effective inhibitors to target RET is of utmost importance. Small molecules have shown promise as inhibitors by binding to the kinase domain of RET and blocking its enzymatic activity. However, the emergence of resistance due to single amino acid changes poses a significant challenge. In this study, a structure-based dynamic pharmacophore-driven approach using E-pharmacophore modeling from molecular dynamics trajectories is proposed to select low-energy favorable hypotheses, and ML-trained QSAR models to predict pIC50 values of compounds. For this aim, extensive small molecule libraries were screened using developed ligand-based models, and potent compounds that are capable of inhibiting RET activation were proposed.

Towards the "Eldorado" of pKa Determination: A Reliable and Rapid DFT Model.

The selection of a "perfect tool" for the theoretical determination of acid-base dissociation constants (Ka) is still puzzling. Recently, we developed a user-friendly model exploiting CAM-B3LYP for determining pKa with impressive reliability. Herein, a new challenge is faced, examining a panel of functionals belonging to different rungs of the "Jacob's ladder" organization, which classifies functionals according to their level of theory. Specifically, meta-generalized gradient approximations (GGAs), hybrid-GGAs, and the more complex range-separated hybrid (RSH)-GGAs were investigated in predicting the pKa of differently substituted carboxylic acids. Therefore, CAM-B3LYP, WB97XD, B3PW91, PBE1PBE, PBEPBE and TPSSTPSS were used, with 6-311G+(d,p) as the basis set and the solvation model based on density (SMD). CAM-B3LYP showed the lowest mean absolute error value (MAE = 0.23) with relatively high processing time. PBE1PBE and B3PW91 provided satisfactory predictions (MAE = 0.34 and 0.38, respectively) with moderate computational time cost, while PBEPBE, TPSSTPSS and WB97XD led to unreliable results (MAE > 1). These findings validate the reliability of our model in predicting carboxylic acids pKa, with MAE well below 0.5 units, using a simplistic theoretical level and a low-cost computational approach.

A molecular arm: the molecular bending-unbending mechanism of integrin.

The balance of integrin activation and deactivation regulates its function and mediates cell behaviors. Mechanical force triggers the unbending and activation of integrin. However, how an activated and extended integrin spontaneously bends back is unclear. I performed all-atom molecular dynamics simulations on an integrin or its subunits to reveal the bending-unbending mechanism of integrin. According to the simulations, the integrin structure works like a human arm. The integrin α subunit serves as the bones, while the ß leg serves as the bicep. The integrin extension results in the stretching of the ß leg, and the extended integrin spontaneously bends as a consequence of the contraction of the ß leg. This study provides new insights into the mechanism of how the integrin secures in the bent inactivated state and sheds light on how the integrin could achieve a stable extended state.

Exploring the potential of high-resolution LC-MS in combination with ion mobility separation and surrogate minimal depth for enhanced almond origin authentication.

Almonds (Prunus dulcisMill.) are consumed worldwide and their geographical origin plays a crucial role in determining their market value. In the present study, a total of 250 almond reference samples from six countries (Australia, Spain, Iran, Italy, Morocco, and the USA) were non-polar extracted and analyzed by UPLC-ESI-IM-qToF-MS. Four harvest periods, more than 30 different varieties, including both sweet and bitter almonds, were considered in the method development. Principal component analysis showed that there are three groups of samples with similarities: Australia/USA, Spain/Italy and Iran/Morocco. For origin determination, a random forest achieved an accuracy of 88.8 %. Misclassifications occurred mainly between almonds from the USA and Australia, due to similar varieties and similar external influences such as climate conditions. Metabolites relevant for classification were selected using Surrogate Minimal Depth, with triacylglycerides containing oxidized, odd chained or short chained fatty acids and some phospholipids proven to be the most suitable marker substances. Our results show that focusing on the identified lipids (e. g., using a QqQ-MS instrument) is a promising approach to transfer the origin determination of almonds to routine analysis.

Efficacy of Noninvasive Brain Stimulation in Treating General Psychopathology Symptoms in Schizophrenia: A Meta-Analysis.

OBJECTIVES: Noninvasive brain stimulation (NIBS) has been shown to effectively alleviate negative and positive symptoms in patients with schizophrenia. However, its impact on depressive symptoms and general psychopathology symptoms (GPSs), which are crucial for functional outcomes, remains uncertain. We aimed to compare the efficacy of various NIBS interventions in treating depressive symptoms and GPSs. METHODS: We conducted a comprehensive search of multiple databases and performed a meta-analysis to evaluate the efficacy of NIBS in treating depressive symptoms and GPSs in schizophrenia. The effect sizes of NIBS for depression symptoms and GPSs were estimated using standard mean differences (SMDs) with 95% confidence intervals (CIs). Subgroup analyses were employed to examine potential influencing factors on the pooled SMD of NIBS for GPSs. RESULTS: Our search yielded 35 randomized controlled trials involving 1715 individuals diagnosed with schizophrenia. The protocol of this systematic review was registered with INPLASY (protocol ID: INPLASY202320082). Neither repetitive transcranial magnetic stimulation (rTMS) nor transcranial direct current stimulation (tDCS) demonstrated significant improvements in depressive symptoms compared to sham controls. NIBS exhibited a small-to-moderate effect size for GPSs, with a pooled SMD of -0.2956 (95% CI: -0.459 to -0.132) and a heterogeneity (I2) of 58.9% (95% CI: 41.5% to 71.1%; p < 0.01) based on a random-effects model. Subgroup analyses of different types of NIBS, different frequencies of rTMS, and different stimulation sites of rTMS revealed no significant differences. Only sex had a significant influence on the effect size of NIBS for general psychopathology symptoms (p < 0.05). However, rTMS might be superior to tDCS, and high-frequency rTMS outperformed low-frequency rTMS in treating GPSs. CONCLUSIONS: We found a small-to-moderate effect size of NIBS in alleviating GPSs in patients with schizophrenia. Both rTMS and tDCS were more effective than sham stimulation in reducing GPSs in schizophrenia. The frequency used was associated with rTMS efficacy for GPSs.

Easy to Use DFT Approach for Computational pKa Determination of Carboxylic Acids.

In pKa computational determination, the challenge in exploring and fostering new methodologies and approaches goes in parallel with the amelioration of computational performances. In this paper a "ready to use methodology" has been compared to other strategies, such as the re-shaping in solvation cavity (Bondi radius re-shaping), wanting to assess its reliability in predicting the pKa of a broad list of carboxylic acids. Thus, the functionals B3LYP and CAM-B3LYP have been selected, using SMD as continuum solvation model. Exploiting our previous results, two water molecules were made explicit on the reaction centre. Data show that our model (CAM-B3LYP/2H2 O) is capable to accurately predict pKa, leading to mean absolute error (MAE) values lower than 0.5. Noteworthy, good results were achieved in computing the pKa of substituents bearing nitro and cyano groups. Focusing on B3LYP, eventually remarkable outputs were obtained only when Bondi correction was applied to the complex with two water molecules. Hence, massive outcomes were obtained in foreseeing the trichloro and trifluoro acetic acid pKa. These findings demonstrated that no complex level of theory nor external factor is required to accurately predict carboxylic acids pKa, with MAE well below 0.5 units.

Application of chemometric tools in the QSAR development of VOC removal in plastic waste recycling.

Deodorization and, in a broader sense, the removal of volatile organic compounds (VOCs) from plastic waste have become increasingly important in the field of plastic recycling, and various new decontamination techniques have been developed. Both in research and industrial practice, the selection of VOCs has been random or unsubstantiated, making it difficult to compare studies and assess decontamination processes objectively. Thus, this study proposes the use of Statistical Molecular Design (SMD) and Quantitative Structure - Activity Relationship (QSAR) as chemometric tools for the selection of representative VOCs, based on physicochemical properties. Various algorithms are used for SMD; hence, several frequently used D-Optimal Onion Design (DOOD) and Space-Filling (SF) algorithms were assessed. Hereby, it was validated that DOOD, by dividing the layers based on the equal-distance approach without so-called 'Adjacent Layer Bias', results in the most representative selection of VOCs. QSAR models that describe VOC removal by water-based washing of plastic waste as a function of molecular weight, polarizability, dipole moment and Hansen Solubility Parameters Distance were successfully established. An adjusted-R2 value of 0.77 ± 0.09 and a mean absolute error of 24.5 ± 4 % was obtained. Consequently, by measuring a representative selection of VOCs compiled using SMD, the removal of other unanalyzed VOCs was predicted on the basis of the QSAR. Another advantage of the proposed chemometric selection procedure is its flexibility. SMD allows to extend or modify the considered dataset according to the available analytical techniques, and to adjust the considered physicochemical properties according to the intended process.

Gender-Based Differential Item Function for the Positive and Negative Semantic Dimensions of the Relationship Satisfaction Scale with Item Response Theory.

Relationship satisfaction is at the core of a robust social life and is essential to mental health. The positive and negative semantic dimensions of the relationship satisfaction (PN-SMD) scale is considered in the field of relationship studies to be a reliable tool for assessing the quality of a person's interpersonal relationships. This study evaluated the psychometric properties of the PN-SMD scale by conducting multidimensional item response theory (MIRT) and differential item functioning (DIF) analyses, both of which are emerging assessment methods that focus on individual items. We recruited 511 Chinese undergraduate students for this study. Construct validity, internal consistency, and concurrent validity were assessed, and MIRT and DIF analyses were conducted. Five of the 14 items were found to have gender-based DIF traits, affecting the scale's construct validity. A revised nine-item scale (DIF items excluded) had a significantly better model fit and demonstrated comparable concurrent validity to the original scale. The implications of our results and future research directions are discussed.

Bioinformatics, thermodynamics, and mechanical resistance of the FtsZ-ZipA complex of Escherichia coli supports a highly dynamic protein interaction in the divisome.

In most microorganisms, cell division is guided by the divisome, a multiprotein complex that assembles at the equator of the cell and is responsible for the synthesis of new cell wall material. FtsZ, the first protein to assemble into this complex forms protofilaments in the cytosol which are anchored to the inner side of the cytosolic membrane by the proteins ZipA and FtsA. FtsZ protofilaments generate a force that deforms the cytosolic membrane and may contribute to the constriction force that leads to the septation of the cell. It has not been studied yet how the membrane protein anchors respond to this force generated by FtsZ. Here we studied the effect of force in the FtsZ-ZipA interaction. We used SMD and obtained the distance to the transition state of key interacting amino acids and SASA of FtsZ and ZipA through the dissociation. The SMD mechanism was corroborated by ITC, and the thermodynamic parameters ΔG0, ΔH0 and ΔS0 were obtained. Finally, we used force spectroscopy by optical tweezers to determine the lifetime of the interaction and rupture probability and their dependence on force at single molecule level. We also obtained the transition state distance, and free energy of the interaction. With the gathering of structural, thermodynamic, kinetic and force parameters we conclude that interaction between FtsZ and ZipA proteins is consistence with the highly dynamic treadmilling process and at least seven ZipA molecules are required to bind to a FtsZ protofilaments to transduce a significant force.

In-silicon studies on hydration in EcoRI-cognate DNA complex.

Restriction endonucleases (REs) cleave DNA at specific site in presence of Mg2+ ion. Experiments further emphasize the role of hydration in metal ion specificity and sequence specificity of DNA cleavage. However, the relation between hydration and specificity has not been understood till date. This leads us to study via all-atom molecular dynamics (MD) simulations how the hydration around the scissile phosphate group changes in presence of Mg2+ and Ca2+ and depend on the DNA sequence. We observe the least number of hydrogen bonds around the scissile phosphate group in presence of Mg2+ ion. We further find that the hydrogen bonds decrease at the scissile phosphate on mutating one base pair in the cleavage region of the DNA in Mg2+ loaded EcoRI-DNA complex. We also perform steered MD simulations and observe that the rate of decrease of fraction of hydrogen bonds is slower in the mutated complex than the unmutated complex.

Comparative Analysis of LC-ESI-IM-qToF-MS and FT-NIR Spectroscopy Approaches for the Authentication of Organic and Conventional Eggs.

The importance of animal welfare and the organic production of chicken eggs has increased in the European Union in recent years. Legal regulation for organic husbandry makes the production of organic chicken eggs more expensive compared to conventional husbandry and thus increases the risk of food fraud. Therefore, the aim of this study was to develop a non-targeted lipidomic LC-ESI-IM-qToF-MS method based on 270 egg samples, which achieved a classification accuracy of 96.3%. Subsequently, surrogate minimal depth (SMD) was applied to select important variables identified as carotenoids and lipids based on their MS/MS spectra. The LC-MS results were compared with FT-NIR spectroscopy analysis as a low-resolution screening method and achieved 80.0% accuracy. Here, SMD selected parts of the spectrum which are associated with lipids and proteins. Furthermore, we used SMD for low-level data fusion to analyze relations between the variables of the LC-MS and the FT-NIR spectroscopy datasets. Thereby, lipid-associated bands of the FT-NIR spectrum were related to the identified lipids from the LC-MS analysis, demonstrating that FT-NIR spectroscopy partially provides similar information about the lipidome. In future applications, eggs can therefore be analyzed with FT-NIR spectroscopy to identify conspicuous samples that can subsequently be counter-tested by mass spectrometry.

[Transfusions and iron chelation in myelodysplastic syndromes]. / Transfusions et chélation du fer dans les syndromes myélodysplasiques.

Iron overload (IO) is probably as toxic in elderly patients with low-risk myelodysplastic syndromes (MDS) as in young thalassemic patients. This impact is more difficult to demonstrate because of associated comorbidities. Cardiovascular disease increases vulnerability to the toxic effects of IO. In recent years, registry studies have shown a survival benefit of Iron Chelation Therapy (ICT) in these patients. These findings are now corroborated by an improvement in event-free survival in a single randomized study: the Telesto study. The EFS curves separate after two years of follow-up. This indicates inertia in the occurrence of complications. The benefits of ICT are also very slowly being revealed. It is possible to offer ICT to patients with transfusion-dependent MDS with a life expectancy of at least two years. In Telesto, patients had a serum ferritin (F) level of at least 1000ng/mL, recommendations using this F threshold as a trigger for chelation seem to be reinforced. It remains an open question whether chelation should be started earlier for effective suppression of IO-related oxidative stress. ICTs could be used in transfusion-dependent MDS patients with life expectancy greater than two years. including possibly higher risk patients responding to hypomethylating agents.

Calculating the Aqueous pKa of Phenols: Predictions for Antioxidants and Cannabinoids.

We aim to develop a theoretical methodology for the accurate aqueous pKa prediction of structurally complex phenolic antioxidants and cannabinoids. In this study, five functionals (M06-2X, B3LYP, BHandHLYP, PBE0, and TPSS) and two solvent models (SMD and PCM) were combined with the 6-311++G(d,p) basis set to predict pKa values for twenty structurally simple phenols. None of the direct calculations produced good results. However, the correlations between the calculated Gibbs energy difference of each acid and its conjugate base, ΔGaq(BA)°=ΔGaqA-°-ΔGaq(HA)°, and the experimental aqueous pKa values had superior predictive accuracy, which was also tested relative to an independent set of ten molecules of which six were structurally complex phenols. New correlations were built with twenty-seven phenols (including the phenols with experimental pKa values from the test set), which were used to make predictions. The best correlation equations used the PCM method and produced mean absolute errors of 0.26-0.27 pKa units and R2 values of 0.957-0.960. The average range of predictions for the potential antioxidants (cannabinoids) was 0.15 (0.25) pKa units, which indicates good agreement between our methodologies. The new correlation equations could be used to make pKa predictions for other phenols in water and potentially in other solvents where they might be more soluble.

[Treating high-risk myelodysplastic syndromes]. / Traitement des syndromes myélodysplasiques de haut risque.

Myelodysplastic syndromes (MDS) are clonal stem cell diseases that primarily affect the elderly. They are classified into low- and high-risk MDS according to prognostic scoring systems. In high-risk patients, treatment should aim to modify the course of the disease by preventing progression to acute myeloid leukemia, and thus improve survival. Stem cell transplantation remains the only curative treatment when possible, but this concerns a small minority of patients. Treatment is mainly based on hypomethylating agents (HMA). Our understanding of the biology of MDS has led to the development of drugs targeting key cellular processes such as apoptosis or post-translational modifications of proteins, the microenvironment and genetic mutations. Currently, new drugs are mainly tested in combination with HMAs in several clinical trials and, although none has yet obtained marketing authorization, many molecules seem promising.

[MDS & CMML: Diagnostic and classification]. / SMD & LMMC : diagnostic et classification.

In 2023, a diagnosis process of myelodysplastic syndrome (MDS) or chronic myelomonocytic leukemia (CMML) is mainly based on morphological results obtained on bone marrow and blood smears which could be completed by cytogenetical analyses. Due to recent finding, flow cytometry data are recognized as useful for the diagnosis of CMML especially. Actual classifications and prognostic scoring systems have changed and nowadays include results of high-throughput sequencing approaches in addition to cytogenetical results. All together, these data allow the medical world to correctly evaluate the prognosis of these patients and to provide some information for targeted therapies. This chapter will provide the most important modifications recently published in the field of diagnosis and prognosis of MDS and CMML.