Monoallelic and bi-allelic variants in NCDN cause neurodevelopmental delay, intellectual disability, and epilepsy.

Neurochondrin (NCDN) is a cytoplasmatic neural protein of importance for neural growth, glutamate receptor (mGluR) signaling, and synaptic plasticity. Conditional loss of Ncdn in mice neural tissue causes depressive-like behaviors, impaired spatial learning, and epileptic seizures. We report on NCDN missense variants in six affected individuals with variable degrees of developmental delay, intellectual disability (ID), and seizures. Three siblings were found homozygous for a NCDN missense variant, whereas another three unrelated individuals carried different de novo missense variants in NCDN. We assayed the missense variants for their capability to rescue impaired neurite formation in human neuroblastoma (SH-SY5Y) cells depleted of NCDN. Overexpression of wild-type NCDN rescued the neurite-phenotype in contrast to expression of NCDN containing the variants of affected individuals. Two missense variants, associated with severe neurodevelopmental features and epilepsy, were unable to restore mGluR5-induced ERK phosphorylation. Electrophysiological analysis of SH-SY5Y cells depleted of NCDN exhibited altered membrane potential and impaired action potentials at repolarization, suggesting NCDN to be required for normal biophysical properties. Using available transcriptome data from human fetal cortex, we show that NCDN is highly expressed in maturing excitatory neurons. In combination, our data provide evidence that bi-allelic and de novo variants in NCDN cause a clinically variable form of neurodevelopmental delay and epilepsy, highlighting a critical role for NCDN in human brain development.

Large-scale genomic investigation of pediatric cholestasis reveals a novel hepatorenal ciliopathy caused by PSKH1 mutations.

PURPOSE: Pediatric cholestasis is the phenotypic expression of clinically and genetically heterogeneous disorders of bile acid synthesis and flow. Although a growing number of monogenic causes of pediatric cholestasis have been identified, the majority of cases remain undiagnosed molecularly. METHODS: In a cohort of 299 pediatric participants (279 families) with intrahepatic cholestasis, we performed exome sequencing as a first-tier diagnostic test. RESULTS: A likely causal variant was identified in 135 families (48.56%). These comprise 135 families that harbor variants spanning 37 genes with established or tentative links to cholestasis. In addition, we propose a novel candidate gene (PSKH1) (HGNC:9529) in 4 families. PSKH1 was particularly compelling because of strong linkage in 3 consanguineous families who shared a novel hepatorenal ciliopathy phenotype. Two of the 4 families shared a founder homozygous variant, whereas the third and fourth had different homozygous variants in PSKH1. PSKH1 encodes a putative protein serine kinase of unknown function. Patient fibroblasts displayed abnormal cilia that are long and show abnormal transport. A homozygous Pskh1 mutant mouse faithfully recapitulated the human phenotype and displayed abnormally long cilia. The phenotype could be rationalized by the loss of catalytic activity observed for each recombinant PSKH1 variant using in vitro kinase assays. CONCLUSION: Our results support the use of genomics in the workup of pediatric cholestasis and reveal PSKH1-related hepatorenal ciliopathy as a novel candidate monogenic form.

Computational investigation of the increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7.

New variants of SARS-CoV-2 are being reported worldwide. The World Health Organization has reported Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.1.529) as the variants of concern. There are speculations that the variants might evade the host immune responses induced by currently available vaccines and develop resistance to drugs under consideration. The first step of viral infection in COVID-19 occurs through the interaction of the spike protein's receptor-binding domain (RBD) with the peptidase domain of the human ACE-2 (hACE-2) receptor. This study aims to get a molecular-level understanding of the mechanism behind the increased infection rate in the alpha variant. We have computationally studied the spike protein interaction in both the wild-type and B.1.1.7 variant with the hACE-2 receptor using molecular dynamics and MM-GBSA based binding free energy calculations. The binding free energy difference shows that the mutant variant of the spike protein has increased binding affinity for the hACE-2 receptor (i.e. ΔG(N501Y,A570D) is in the range -7.2 to -7.6 kcal mol-1) and the results were validated using Density functional theory. We demonstrate that with the use of state-of-the-art computational approaches, we can, in advance, predict the virulent nature of variants of SARS-CoV-2 and alert the world healthcare system.

Correction: Computational investigation of the increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7.

Correction for 'Computational investigation of the increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7' by N. Arul Murugan et al., Phys. Chem. Chem. Phys., 2022, 24, 20371-20380, https://doi.org/10.1039/D2CP00469K.

Isolation, Characterization, and Medicinal Potential of Polysaccharides of Morchella esculenta.

Mushroom polysaccharides are active medicinal compounds that possess immune-modulatory and anticancer properties. Currently, the mushroom polysaccharides krestin, lentinan, and polysaccharopeptides are used as anticancer drugs. They are an unexplored source of natural products with huge potential in both the medicinal and nutraceutical industries. The northern parts of Pakistan have a rich biodiversity of mushrooms that grow during different seasons of the year. Here we selected an edible Morchella esculenta (true morels) of the Ascomycota group for polysaccharide isolation and characterization. Polysaccharopeptides and polysaccharides from this mushroom were isolated using the green chemistry, hot water treatment method. Fourier transform infrared spectroscopy revealed the sugar nature and possible beta-glucan type structure of these polysaccharides. Antioxidant assays showed that the deproteinized polysaccharides have moderate free radical scavenging activity. These isolated polysaccharides exhibited good acetylcholinesterase (AChE) and butyryl cholinesterase (BChE) inhibition activities. Therefore, these polysaccharides may be valuable for the treatment of Alzheimer's and Parkinson's diseases. Further bioassays are needed to discover the true potential of M. esculenta polysaccharides for medicinal purposes.

Antimicrobial and antioxidant activities of silver nanoparticles synthesized by novel biogenic method using mixed reductants.

A novel method, for the synthesis of silver nanoparticles that are eco-friendly by means of mixed reductants method, has been developed. The combined extract of Mentha viridis plant and Prunus domestica gum were used as reducing agents for the synthesis of silver nanoparticles of the size less than 40 nm in diameter. The effect of time and concentration on the formation of silver nanoparticles were also monitored. The silver nanoparticles formed were verified by surface Plasmon spectra using single and double beam UV-Vis spectrophotometer. The XRD technique and scanning electron microscopy were performed to analyze the crystalline structure, crystallite size and morphology. The synthesized silver nanoparticles were tested against different bacterial and fungus strains. The silver nanoparticles showed good inhibition in antimicrobial study and low MIC for bacterial strains. The antioxidant assay was performed to check the scavenging activity. In DPPH, the silver nanoparticles showed good scavenging activity and were found close to that of ascorbic acid.

Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition.

BACKGROUND: The disco-interacting protein 2 homolog C (DIP2C) gene is an uncharacterized gene found mutated in a subset of breast and lung cancers. To understand the role of DIP2C in tumour development we studied the gene in human cancer cells. METHODS: We engineered human DIP2C knockout cells by genome editing in cancer cells. The growth properties of the engineered cells were characterised and transcriptome and methylation analyses were carried out to identify pathways deregulated by inactivation of DIP2C. Effects on cell death pathways and epithelial-mesenchymal transition traits were studied based on the results from expression profiling. RESULTS: Knockout of DIP2C in RKO cells resulted in cell enlargement and growth retardation. Expression profiling revealed 780 genes for which the expression level was affected by the loss of DIP2C, including the tumour-suppressor encoding CDKN2A gene, the epithelial-mesenchymal transition (EMT) regulator-encoding ZEB1, and CD44 and CD24 that encode breast cancer stem cell markers. Analysis of DNA methylation showed more than 30,000 sites affected by differential methylation, the majority of which were hypomethylated following loss of DIP2C. Changes in DNA methylation at promoter regions were strongly correlated to changes in gene expression, and genes involved with EMT and cell death were enriched among the differentially regulated genes. The DIP2C knockout cells had higher wound closing capacity and showed an increase in the proportion of cells positive for cellular senescence markers. CONCLUSIONS: Loss of DIP2C triggers substantial DNA methylation and gene expression changes, cellular senescence and epithelial-mesenchymal transition in cancer cells.

Computational and molecular tools for scalable rAAV-mediated genome editing.

The rapid discovery of potential driver mutations through large-scale mutational analyses of human cancers generates a need to characterize their cellular phenotypes. Among the techniques for genome editing, recombinant adeno-associated virus (rAAV)-mediated gene targeting is suited for knock-in of single nucleotide substitutions and to a lesser degree for gene knock-outs. However, the generation of gene targeting constructs and the targeting process is time-consuming and labor-intense. To facilitate rAAV-mediated gene targeting, we developed the first software and complementary automation-friendly vector tools to generate optimized targeting constructs for editing human protein encoding genes. By computational approaches, rAAV constructs for editing ~71% of bases in protein-coding exons were designed. Similarly, ~81% of genes were predicted to be targetable by rAAV-mediated knock-out. A Gateway-based cloning system for facile generation of rAAV constructs suitable for robotic automation was developed and used in successful generation of targeting constructs. Together, these tools enable automated rAAV targeting construct design, generation as well as enrichment and expansion of targeted cells with desired integrations.

Protein tyrosine phosphatase 1B inhibitors isolated from Artemisia roxburghiana.

Artemisia roxburghiana is used in traditional medicine for treating various diseases including diabetes. The present study was designed to evaluate the antidiabetic potential of active constituents by using protein tyrosine phosphatase 1B (PTP1B) as a validated target for management of diabetes. Various compounds were isolated as active principles from the crude methanolic extract of aerial parts of A. roxburghiana. All compounds were screened for PTP1B inhibitory activity. Molecular docking simulations were performed to investigate the mechanism behind PTP1B inhibition of the isolated compound and positive control, ursolic acid. Betulinic acid, betulin and taraxeryl acetate were the active PTP1B principles with IC50 values 3.49 ± 0.02, 4.17 ± 0.03 and 87.52 ± 0.03 µM, respectively. Molecular docking studies showed significant molecular interactions of the triterpene inhibitors with Gly220, Cys215, Gly218 and Asp48 inside the active site of PTP1B. The antidiabetic activity of A. roxburghiana could be attributed due to PTP1B inhibition by its triterpene constituents, betulin, betulinic acid and taraxeryl acetate. Computational insights of this study revealed that the C-3 and C-17 positions of the compounds needs extensive optimization for the development of new lead compounds.

Phytochemicals from Dodonaea viscosa and their antioxidant and anticholinesterase activities with structure-activity relationships.

Context Dodonaea viscosa (L.) Jacq (Sapindaceae) has been used in traditional medicine as antimalarial, antidiabetic and antibacterial agent, but further investigations are needed. Objective This study determines the antioxidant and anticholinesterase activities of six compounds (1-6) and two crystals (1A and 3A) isolated from D. viscosa, and discusses their structure-activity relationships. Materials and methods Antioxidant activity was evaluated using six complementary tests, i.e., ß-carotene-linoleic acid; DPPH(•), ABTS(•+), superoxide scavenging, CUPRAC and metal chelating assays. Anticholinesterase activity was performed using the Elman method. Results Clerodane diterpenoids (1 and 2) and phenolics (3-6) - together with three crystals (1A, 3A and 7A) - were isolated from the aerial parts of D. viscosa. Compound 3A exhibited good antioxidant activity in DPPH (IC50: 27.44 ± 1.06 µM), superoxide (28.18 ± 1.35% inhibition at 100 µM) and CUPRAC (A0.5: 35.89 ± 0.09 µM) assays. Compound 5 (IC50: 11.02 ± 0.02 µM) indicated best activity in ABTS assay, and 6 (IC50: 14.30 ± 0.18 µM) in ß-carotene-linoleic acid assay. Compounds 1 and 3 were also obtained in the crystal (1A and 3A) form. Both crystals showed antioxidant activity. Furthermore, crystal 3A was more active than 3 in all activity tests. Phenol 6 possessed moderate anticholinesterase activity against acetylcholinesterase and butyrylcholinesterase enzymes (IC50 values: 158.14 ± 1.65 and 111.60 ± 1.28 µM, respectively). Discussion and conclusion This is the first report on antioxidant and anticholinesterase activities of compounds 1, 2, 5, 6, 1A and 3A, and characterisation of 7A using XRD. Furthermore, the structure-activity relationships are also discussed in detail for the first time.

In situ sequencing identifies TMPRSS2-ERG fusion transcripts, somatic point mutations and gene expression levels in prostate cancers.

Translocations contribute to the genesis and progression of epithelial tumours and in particular to prostate cancer development. To better understand the contribution of fusion transcripts and visualize the clonal composition of multifocal tumours, we have developed a technology for multiplex in situ detection and identification of expressed fusion transcripts. When compared to immunohistochemistry, TMPRSS2-ERG fusion-negative and fusion-positive prostate tumours were correctly classified. The most prevalent TMPRSS2-ERG fusion variants were visualized, identified, and quantitated in human prostate cancer tissues, and the ratio of the variant fusion transcripts could for the first time be directly determined by in situ sequencing. Further, we demonstrate concurrent in situ detection of gene expression, point mutations, and gene fusions of the prostate cancer relevant targets AMACR, AR, TP53, and TMPRSS2-ERG. This unified approach to in situ analyses of somatic mutations can empower studies of intra-tumoural heterogeneity and future tissue-based diagnostics of mutations and translocations.

Variation of groundwater and mineral composition of in situ leaching uranium in Bayanwula mining area, China.

The reaction between the lixiviant and the minerals in the aquifer of In-situ uranium leaching (ISL) will result mineral dissolution and precipitation. ISL will cause changes in the chemical composition of groundwater and the porosity and permeability of aquifer, as well as groundwater pollution. Previous studies lack three-dimension numerical simulation that includes a variety of minerals and considers changes in porosity and permeability properties simultaneously. To solve these problems, a three-dimensional reactive transport model (RTM) which considered minerals, main water components and changes in porosity and permeability properties in Bayanwula mine has been established. The results revealed that: (1) Uranium elements were mainly distributed inside the mining area and had a weak trend of migration to the outside. The strong acidity liquid is mainly in the mining area, and the acidity liquid dissolved the minerals during migrating to the outside of the mining area. The concentration front of major metal cations such as K+, Na+, Ca2+ and Mg2+ is about 150m away from the boundary. (2) The main dissolved minerals include feldspar, pyrite, calcite, sodium montmorillonite and calcium montmorillonite. Calcite is the most soluble mineral and one of the sources of gypsum precipitation. Other minerals will dissolve significantly after calcite is dissolved. (3) ISL will cause changes in porosity and permeability of the mining area. Mineral dissolution raises porosity and permeability near the injection well. Mineral precipitation reduced porosity and permeability near the pumping well, which can plugging the pore throat and affect recovery efficiency negatively.

Promoting local production and active pharmaceutical ingredient (API) industry in low and middle income countries (LMICs): impact on medicines access and policy.

The success of universal coverage depends on ensuring that patients have access to medicine. Encouraging local production of medicines in developing countries can provide better access to medicines. In addition to determining the quality of pharmaceutical goods, Active Pharmaceutical Ingredients (APIs) also determine their cost. According to market forecasts, the active pharmaceutical ingredients market is expected to increase from USD 193.15 billion in 2023 to USD 285.29 billion by 2028. Pakistan largely depends on India and China for its Active Pharmaceutical Ingredient requirements. It was feared that a shortage of medicines would result from Pakistan's government suspending all trade with India on August 9, 2019. To improve health security in Pakistan, the Government of Pakistan has introduced an API promotion Policy in 2022. Financial and non-financial incentives have helped many countries develop their API industries like China, India, and Bangladesh. The current domestic API market of Pakistan is around 150 million $. After the introduction of the policy, the existing units are increasing their capacity while eight new API units are in the process of establishment. Through local production of APIs and intermediates, Pakistan can improve its health security by learning from the experiences of neighbouring countries, especially China.

Smart integration of cold plasma stream and surface discharge with ns laser ablation for composite nanomaterial.

In this paper, smart integration of cold dielectric barrier discharge (DBD) plasma in various geometrical arrangements with laser ablation at atmospheric pressure for nanomaterial was described. A composite Co:ZnO target was ablated in an airflow by a nanosecond (ns) laser (wavelength: 1064 nm, pulse duration: 30 ns) using fluence of 5 J-cm-2 at a repetition rate of 10 Hz. The nanomaterial produced under vertical and oblique plasma streams, surface discharge and gas flow, were compared. Utilization surface discharge markedly improved the material adhesion by altering surface intrinsic behavior, inducing anticipated surface energy activation, chemical changes, and the formation of a densely packed solid structure. Under all conditions, the material consistently retained its crystalline nature, elemental composition, and ultraviolet emission characteristics. These preliminary findings hold promise for additional research, suggesting avenues for making complex materials in a flexible environment. Such new advancements could facilitate applications in the biomedical, catalysis, pharmaceutical, and surgical device domains.

Analyzing solitary wave solutions of the nonlinear Murray equation for blood flow in vessels with non-uniform wall properties.

Solitary wave solutions are of great interest to bio-mathematicians and other scientists because they provide a basic description of nonlinear phenomena with many practical applications. They provide a strong foundation for the development of novel biological and medical models and therapies because of their remarkable behavior and persistence. They have the potential to improve our comprehension of intricate biological systems and help us create novel therapeutic approaches, which is something that researchers are actively investigating. In this study, solitary wave solutions of the nonlinear Murray equation will be discovered using a modified extended direct algebraic method. These solutions represent a uniform variation in blood vessel shape and diameter that can be used to stimulate blood flow in patients with cardiovascular disease. These solutions are newly in the literature, and give researchers an important tool for grasping complex biological systems. To see how the solitary wave solutions behave, graphs are displayed using Matlab.

Biological investigations of Aspergillus ficuum via in vivo, in vitro and in silico analyses.

Serious human health impacts have been observed worldwide due to several life-threatening diseases such as cancer, candidiasis, hepatic coma, and gastritis etc. Exploration of nature for the treatment of such fatal diseases is an area of immense interest for the scientific community. Based on this idea, the genus Aspergillus was selected to discover its hidden therapeutic potential. The genus Aspergillus is known to possess several biologically active compounds. The current research aimed to assess the biological and pharmacological potency of the extracts of less-studied Aspergillus ficuum (FCBP-DNA-1266) (A. ficuum) employing experimental and bioinformatics approaches. The disc diffusion method was used for the antifungal investigation, and the MTT assay was performed to assess the anticancer effects. Mice were employed as an in vivo model to evaluate the antispasmodic effects. A standard spectrophotometric technique was applied to gauge the urease inhibitory activity. The antifungal studies indicate that both n-hexane and ethyl acetate extracts were significantly active against Candida albicans (C. albicans) with their zone of inhibitions (ZOI) values reported as 19 ± 1.06 mm and 25 ± 0.55 mm, respectively at a dose of 30 µg.mL-1. In vitro cytotoxicity assay against HeLa, fibroblast 3T3, prostate PC3, and breast MCF-7 cancer cell lines was performed. The ethyl acetate extract of A. ficuum was found to be significantly active against MCF-7 with its IC50 value of 43.88 µg.mL-1. However, no substantial effects on the percent cell death of HeLa cancer cell lines were observed. In addition, the A. ficuum extracts also inhibited the urease enzyme compared to standard thiourea. The antispasmodic activity of A. ficuum extract was assessed by an in vivo model and the results demonstrated promising activity at 150 mg.kg-1. Molecular docking results also supported the antifungal, anticancer, and antiurease potency of A. ficuum extract. Overall, the results display promising aspects of A. ficuum extract as a future pharmacological source.

Pharmacovigilance in High-Income Countries: Current Developments and a Review of Literature.

The world bank has classified 80 economies based on their Gross National Income (GNI) per capita as High-Income. European Medicines Agency (EMA), Food and Drug Administration (FDA), and Pharmaceuticals and Medical Devices Agency (PMDA) are the major regulatory stakeholders driving global pharmacovigilance regulations. The purpose of this article is to describe pharmacovigilance systems and processes in high-income countries, particularly those that are also members of the International Conference on Harmonization (ICH). All high-income countries are members of the WHO PIDM. The income level of a country has a direct relationship with medicine safety measures. All ten pioneering members of the Uppsala monitoring centre are from high-income countries and were the first responders after the thalidomide tragedy by making drug evaluation committees, introducing the ADR reporting forms and taking safety measures. Despite access to the VigiBase, some countries have separate databases for managing and analyzing data like Canada Vigilance online database, FDA Adverse Event Reporting System, the French pharmacovigilance database and European Union's system Eudravigilance. All high-income countries have robust pharmacovigilance systems. USFDA and EMA are the world leaders in the field of pharmacovigilance. Most high-income countries follow EMA guidelines. Medicine safety is directly influenced by a country's income level.

Domain Adaptive Object Detection via Balancing Between Self-Training and Adversarial Learning.

Deep learning based object detectors struggle generalizing to a new target domain bearing significant variations in object and background. Most current methods align domains by using image or instance-level adversarial feature alignment. This often suffers due to unwanted background and lacks class-specific alignment. A straightforward approach to promote class-level alignment is to use high confidence predictions on unlabeled domain as pseudo-labels. These predictions are often noisy since model is poorly calibrated under domain shift. In this paper, we propose to leverage model's predictive uncertainty to strike the right balance between adversarial feature alignment and class-level alignment. We develop a technique to quantify predictive uncertainty on class assignments and bounding-box predictions. Model predictions with low uncertainty are used to generate pseudo-labels for self-training, whereas the ones with higher uncertainty are used to generate tiles for adversarial feature alignment. This synergy between tiling around uncertain object regions and generating pseudo-labels from highly certain object regions allows capturing both image and instance-level context during the model adaptation. We report thorough ablation study to reveal the impact of different components in our approach. Results on five diverse and challenging adaptation scenarios show that our approach outperforms existing state-of-the-art methods with noticeable margins.

Potential anticancer and antioxidant lauric acid-based hydrazone synthesis and computational study toward the electronic properties.

The modification of natural products is one of the key areas of synthetic organic chemistry for obtaining valuable chemical building blocks that have medicinal significance. In this study, lauric acid-based hydrazones, namely (E)-N'-(2-nitrobenzylidene)dodecanehydrazide (NBDH), (E)-N'-(naphthalen-1-ylmethylene)dodecanehydrazide (NMDH), and (E)-N'-(4-fluorobenzylidene)dodecanehydrazide (FBDH), were synthesized and characterized using spectroscopic techniques. The newly synthesized lauric acid-based hydrazones were screened for their anticancer and antioxidant potential. The antioxidants showed their activity by inhibiting the oxidative chain reactions that produce reactive oxygen species. The antioxidant activity showed that NBDH exhibited the maximum DPPH inhibitory activity when compared with that of NMDH and FBDH, whereas the anticancer activity showed that FBDH exhibited maximum percent viability when compared to that of NBDH and NMDH. The reactivity and biological needs of the synthesized compounds NBDH, NMDH, and FBDH were met by performing geometrical, FT-IR vibrational, UV-visible, global reactivity parameters (GRP), MEP, FMO, NBO, ELF, LOL, and nonlinear optical (NLO) analysis at the DFT/B3LYP/6-311+G(d,p) level. NBO analysis confirmed the existence of extended conjugation and intramolecular charge transfer among NBDH, NMDH, and FBDH, which have the lowest gap in π → π*, which are in line with the FMO results where successful charge transfer occurred from the highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO). GRP analysis confirmed the potential of NBDH, NMDH, and FBDH for biological, electronic, and NLO applications. It is clear from the comparative analysis of the urea molecule that NBDH, NMDH, and FBDH all comprise fine NLO properties.