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The increasingly large amount of proteomics data in the public domain enables, among other applications, the combined analyses of datasets to create comparative protein expression maps covering different organisms and different biological conditions. Here we have reanalysed public proteomics datasets from mouse and rat tissues (14 and 9 datasets, respectively), to assess baseline protein abundance. Overall, the aggregated dataset contained 23 individual datasets, including a total of 211 samples coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively. In all cases, we studied the distribution of canonical proteins between the different organs. The number of canonical proteins per dataset ranged from 273 (tendon) and 9,715 (liver) in mouse, and from 101 (tendon) and 6,130 (kidney) in rat. Then, we studied how protein abundances compared across different datasets and organs for both species. As a key point we carried out a comparative analysis of protein expression between mouse, rat and human tissues. We observed a high level of correlation of protein expression among orthologs between all three species in brain, kidney, heart and liver samples, whereas the correlation of protein expression was generally slightly lower between organs within the same species. Protein expression results have been integrated into the resource Expression Atlas for widespread dissemination. Author summary: We have reanalysed 23 baseline mass spectrometry-based public proteomics datasets stored in the PRIDE database. Overall, the aggregated dataset contained 211 samples, coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively. We analysed the distribution of protein expression across organs in both species. We also studied how protein abundances compared across different datasets and organs for both species. Then we performed gene ontology and pathway enrichment analyses to identify enriched biological processes and pathways across organs. We also carried out a comparative analysis of baseline protein expression across mouse, rat and human tissues, observing a high level of expression correlation among orthologs in all three species, in brain, kidney, heart and liver samples. To disseminate these findings, we have integrated the protein expression results into the resource Expression Atlas. [ABSTRACT FROM AUTHOR]

Summary: A fundamental question in developmental biology is whether there are mechanisms to detect stem cells with mutations that, although not adversely affecting viability, would compromise their ability to contribute to further development. Here, we show that cell competition is a mechanism regulating the fitness of embryonic stem cells (ESCs). We find that ESCs displaying defective bone morphogenetic protein signaling or defective autophagy or that are tetraploid are eliminated at the onset of differentiation by wild-type cells. This elimination occurs in an apoptosis-dependent manner and is mediated by secreted factors. Furthermore, during this process, we find that establishment of differential c-Myc levels is critical and that c-Myc overexpression is sufficient to induce competitive behavior in ESCs. Cell competition is, therefore, a process that allows recognition and elimination of defective cells during the early stages of development and is likely to play important roles in tissue homeostasis and stem cell maintenance. [Copyright &y& Elsevier]

[Display omitted] • Synthesis of ampyrone based 1,2,3-triazole appended derivative (APT). • Characterization of the synthesized compound via spectroscopic techniques. • Ion sensing analysis of APT via UV–visible and fluorescence spectroscopy. • DFT simulations to obtain energy-minimized structures of APT and APT-Cu(II) complex. • Molecular docking analysis of APT with synaptic vesicle protein (SV2A). The present report describes the application of the 'Click Chemistry' pathway to synthesize a fluorescent probe (APT) based on ampyrone (4-aminoantipyrine), entailing two benzyl groups as the fluorophores coupled to the antipyrine structure through 1,2,3-triazole moieties. Infrared spectroscopy (IR), nuclear magnetic resonance (1H and 13C), and mass spectrometry were the standard spectroscopic methods used to characterize APT. The ion recognition potential of the probe was analyzed through absorption and emission spectroscopy employing a 4:1 combination of CH 3 CN and H 2 O, which demonstrated APT to be an efficient sensing agent for Cu(II) ions, wherein the absorption spectrum of the probe displayed a hypsochromic shift with a hyperchromic shift on gradually adding the metal ion solution of Cu(II), whereas quenching of the probe's fluorescence emission on Cu(II) addition was attributed to the chelation-enhanced fluorescence quenching (CHEQ), induced by the d9 electronic configuration of Cu(II). The stoichiometry of the complexation of APT with Cu(II) is indicative of a 1:1 ratio, while the detection limit (LOD) and quantification limit (LOQ) as estimated from the fluorescence titration results were 3.11 µM and 10.35 µM respectively. Furthermore, DFT analysis was also undertaken to yield the energy-optimized structures and HOMO-LUMO density plots of APT and its corresponding Cu(II) complex via the B3LYP/631G+(d,p) level of theory for APT, and LANL2DZ basis set for the APT-Cu(II) complex. Docking analysis of the probe with the synaptic vesicle protein (SV2A) gave glimpses about its anticonvulsant properties. [ABSTRACT FROM AUTHOR]

This paper represents the synthesis of 1,2,3-triazole hybrid organosilanes as sensors for the detection of F- ions, antibacterial activity and molecular docking analysis in the active sites of DNA gyrase of S. aureus (5CPH). Further, the binding mode of compound 7a with F- was proven by Density functional theory (DFT) calculations. [Display omitted] • 1,2,3-triazole hybrid organosilanes have been synthesized and characterized. • Sensing behavior of the organosilanes were evaluated towards various ions. • The binding mode of compound 7a with F- was proven by DFT calculations. • The prepared compounds showed inhibitory activity against Staphylococcus aureus. • Molecular docking was performed for compound 7a with the active sites of 5CPH. Among various anions, fluoride is one of the most essential because of its use in the treatment of osteoporosis and dental care, but excessive use can have negative effects on human health. Owing to these reasons, the present study addresses the efficient synthesis of 1,2,3-triazole hybrid organosilanes achieved via a copper-catalyzed azide–alkyne cycloaddition (CuAAC) click chemistry followed by the condensation reaction. The synthesized compounds were confirmed by (1H and 13C) NMR spectroscopy and mass spectrometry. The compounds 7a-7b showed high selectivity and sensitivity toward F- ions with limit of detection (LOD) of 1.11 × 10-6 M and 43 × 10-6 M respectively. The binding mode of compound 7a with F- was proven by Density functional theory (DFT) calculations. The in vitro antibacterial activity of synthesized compounds 7a-7b against two gram-negative (Escherichia coli and Pseudomonas aeruginosa) and one gram-positive (Staphylococcus aureus) bacterial strains were determined, and the results exhibited good inhibitory activity against gram-positive (Staphylococcus aureus). Additionally, molecular docking study was carried out to look into the interaction between compound 7a and the active sites of the S. aureus DNA gyrase (5CPH). The docking results revealed the better affinity for protein with binding energy of −6.55 kcal/mol. [ABSTRACT FROM AUTHOR]

When only physicians are trained to insert Coudé catheters, there is an increased burden to both the patient and the providers. Training nurses for placement of Coudé catheters can improve care and allow for better use of health care resources. [ABSTRACT FROM AUTHOR]

This study explored administrators' attitudes about the use of physical restraint in their school settings. Administrators of day treatment and residential programs for elementary students with emotional and behavioral disorders in the Mid-Atlantic states were surveyed on their attitudes toward, and the use of, physical restraint within their programs. Results showed that the use of physical restraint varied widely, ranging from 0 to more than 3 instances per day. About one third of the sample reported between 1 to 3 physical restraints per week. School size was found to be positively correlated with number of restraints, in schools that used physical restraint, more than half employed basket holds and prone restraints, most commonly following physical aggression. Administrators were divided in their opinions about the therapeutic utility of physical restraint, although most stated it was needed to keep schools safe. Recommendations for future research in the area of physical restraint are presented. [ABSTRACT FROM AUTHOR]

The present investigation focused on exploring the potential of fungal endophytes as a valuable source of bioactive compounds with diverse applications. The phenolic compound 5-methylmellein was isolated for the first time from Alternaria burnsii , an endophytic fungus associated with Morus alba Linn. The compounds were structurally characterized using comprehensive spectral analysis, including 1 H-, 13 C, and 2D-NMR, as well as HRESI-MS. The study investigated the antifungal activity of 5-methylmellein against several plant pathogenic fungi, including Botrytis cinerea , Colletotrichum gloeosporioides , Cercospora beticola , and Rhizoctonia solani . In vitro assays showed significant inhibition of various plant pathogenic fungi, and the IC 50 values ranging from 34.59 ± 1.03 a µg/mL to 44.76 ± 1.03 b µg/mL against the tested fungi. In vivo experiments on apples and grapes revealed that 5-Methylmellein significantly reduced fruit decay caused by Botrytis cinerea . The wound incidence in the control group reached 95.78%, while the treated groups exhibited a reduction of 37.54% after 15 days. These findings underscore the potential of 5-methylmellein as a potent antifungal agent, suggesting its eco-friendly application in agriculture for managing fruit decay., Competing Interests: Conflict of interestNo potential conflict of interest was reported by the authors., (© King Abdulaziz City for Science and Technology 2024. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Fungal endophytes are a known warehouse of bioactive compounds with multifarious applications. In the present investigation two compounds, β-Sitosterol (1) and ursolic acid (2), were isolated from Alternaria alternata , an endophytic fungus associated with Morus alba Linn for the first time. The structure of the compounds was elucidated on the basis of comprehensive spectral analysis (UV, IR, 1 H-, 13 C- and 2D-NMR, as well as HRESI-MS). In the in vitro alpha amylase inhibitory assay both compounds (1) and (2) show potent antidiabetic activity. In support, Docking studies indicate significant binding affinity of the isolated compounds. Hence from the present study, it can be concluded that endophytic fungi in Morus alba Linn can find use in antidiabetic drug development in the medicinal industry.Communicated by Ramaswamy H. Sarma.

In this study, two novel chalcone-derived 1,2,3-triazole-appended positional isomers (probe 6 and probe 9) were synthesized via the 'CuAAC' (Cu(i) - catalysed alkyne azide cycloaddition) methodology for the purpose of metal ion detection. The synthesized probes underwent characterization utilizing standard spectroscopic methodologies including FTIR, NMR ( 1 H and 13 C), and mass spectrometry. Subsequently, the sensing capabilities of these probes were explored using UV-Vis and fluorescence spectroscopy, wherein their selective recognition potential was established for Pb(ii) and Cu(ii), both of which can pose serious health hazards when prevalent in the environment above permissible limits. Both the probes exhibited fairly low limits of detection (LoD), determined as 5.69 μM and 6.55 μM in the case of probe 6 for Pb(ii) and Cu(ii) respectively; whereas the probe 9 exhibited an LoD of 5.06 μM and 7.52 μM for Pb(ii) and Cu(ii), respectively. The job's plot for the probe demonstrates the formation of a 1 : 1 complex between the metal and ligand. Furthermore, the interaction of the free probes with the metal ions in the metal-ligand complex was elucidated through 1 H NMR analysis and validated theoretically using Density Functional Theory (DFT) simulations with the B3LYP/6-311G++(d,p) and B3LYP/LANL2DZ basis sets for geometry optimization of the probes and their corresponding metal complexes. These findings offer a reliable approach to Cu(ii) and Pb(ii) ion detection and can be further used for the potential applications in environmental monitoring and analytical chemistry., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

TIICs are critical components of the TME and are used to estimate prognostic and treatment responses in many malignancies. TIICs in the tumor microenvironment are assessed and quantified by categorizing immune cells into three subtypes: CD66b+ tumor-associated neutrophils (TANs), FoxP3+ regulatory T cells (Tregs), and CD163+ tumor-associated macrophages (TAMs). In addition, many cancers have tumor-infiltrating M1 and M2 macrophages, neutrophils (Neu), CD4+ T cells (T-helper), CD8+ T cells (T-cytotoxic), eosinophils, and mast cells. A variety of clinical treatments have linked tumor immune cell infiltration (ICI) to immunotherapy receptivity and prognosis. To improve the therapeutic effectiveness of immune-modulating drugs in a wider cancer patient population, immune cells and their interactions in the TME must be better understood. This study examines the clinicopathological effects of TIICs in overcoming tumor-mediated immunosuppression to boost antitumor immune responses and improve cancer prognosis. We successfully analyzed the predictive and prognostic usefulness of TIICs alongside TMB and ICI scores to identify cancer's varied immune landscapes. Traditionally, immune cell infiltration was quantified using flow cytometry, immunohistochemistry, gene set enrichment analysis (GSEA), CIBERSORT, ESTIMATE, and other platforms that use integrated immune gene sets from previously published studies. We have also thoroughly examined traditional limitations and newly created unsupervised clustering and deconvolution techniques (SpatialVizScore and ProTICS). These methods predict patient outcomes and treatment responses better. These models may also identify individuals who may benefit more from adjuvant or neoadjuvant treatment. Overall, we think that the significant contribution of TIICs in cancer will greatly benefit postoperative follow-up, therapy, interventions, and informed choices on customized cancer medicines.

In modern times, medicine is predominantly based on evidence-based practices, whereas in ancient times, indigenous people relied on plant-based medicines with factual evidence documented in ancient books or folklore that demonstrated their effectiveness against specific infections. Plants and microbes account for 70% of drugs approved by the USFDA (U.S. Food and Drug Administration). Stilbenes, polyphenolic compounds synthesized by plants under stress conditions, have garnered significant attention for their therapeutic potential, bridging ancient wisdom with modern healthcare. Resveratrol, the most studied stilbene, initially discovered in grapes, red wine, peanuts, and blueberries, exhibits diverse pharmacological properties, including cardiovascular protection, antioxidant effects, anticancer activity, and neuroprotection. Traditional remedies, documented in ancient texts like the Ayurvedic Charak Samhita, foreshadowed the medicinal properties of stilbenes long before their modern scientific validation. Today, stilbenes are integral to the booming wellness and health supplement market, with resveratrol alone projected to reach a market value of 90 million US$ by 2025. However, challenges in stilbene production persist due to limited natural sources and costly extraction methods. Bioprospecting efforts reveal promising candidates for stilbene production, particularly endophytic fungi, which demonstrate high-yield capabilities and genetic modifiability. However, the identification of optimal strains and fermentation processes remains a critical consideration. The current review emphasizes the knowledge of the medicinal properties of Stilbenes (i.e., cardiovascular, antioxidant, anticancer, anti-inflammatory, etc.) isolated from plant and microbial sources, while also discussing strategies for their commercial production and future research directions. This also includes examples of novel stilbenes compounds reported from plant and endophytic fungi., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Expression Atlas (www.ebi.ac.uk/gxa) and its newest counterpart the Single Cell Expression Atlas (www.ebi.ac.uk/gxa/sc) are EMBL-EBI's knowledgebases for gene and protein expression and localisation in bulk and at single cell level. These resources aim to allow users to investigate their expression in normal tissue (baseline) or in response to perturbations such as disease or changes to genotype (differential) across multiple species. Users are invited to search for genes or metadata terms across species or biological conditions in a standardised consistent interface. Alongside these data, new features in Single Cell Expression Atlas allow users to query metadata through our new cell type wheel search. At the experiment level data can be explored through two types of dimensionality reduction plots, t-distributed Stochastic Neighbor Embedding (tSNE) and Uniform Manifold Approximation and Projection (UMAP), overlaid with either clustering or metadata information to assist users' understanding. Data are also visualised as marker gene heatmaps identifying genes that help confer cluster identity. For some data, additional visualisations are available as interactive cell level anatomograms and cell type gene expression heatmaps., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Herein, a 1,2,3-triazole derivative (CBT), synthesized using the Copper(i) catalyzed Alkyne Azide Cycloaddition (CuAAC) procedure, based on a chalcone skeleton has been reported, that was implemented as an effective sensor for Pb(ii) and Cu(ii) ions. The synthesized CBT was characterized using spectroscopic techniques such as FTIR, NMR ( 1 H and 13 C), and mass spectrometry. The sensing behaviour of CBT was analyzed using UV-Vis spectroscopy, demonstrating selective sensing for Pb(ii) and Cu(ii) ions, competitively. The correlation plot revealed the detection limit for Pb(ii) and Cu(ii) ions to be 100 μM and 110 μM respectively. In addition, DFT simulations and molecular electrostatic potential (MEP) studies scrutinized the binding strategy of the free CBT and its orientation towards the metal ions in the metal-ligand complex. The probe CBT was predicted via the online platform Way2drug for its pharmacological properties, investigating the possibility to inhibit early atherosclerosis. CBT was subsequently docked to the TRIB1 protein using AutoDock Vina and demonstrated a high binding affinity with a value of -6.2 kcal mol -1 ., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Emergence of trace elements at potentially toxic concentrations in the environment has become a global issue in recent times. Owing to the rapid population growth, unregulated industrialisation, intensive farming practices and excessive mining activities, these elements are accumulating in environment at high toxic concentrations. The exposure of plants to metal-contaminated environments severely influences their reproductive and vegetative growth, eventually affecting crop performance and production. Hence, it is crucial to find alternatives to mitigate the stress caused by toxic elements, in plants of agricultural importance. In this context, silicon (Si) has been widely recognized to alleviate metal toxicity and promote plant growth during various stress conditions. Amending soil with silicates has shown to ameliorate the lethal effects of metals and stimulates crop development. However, in comparison to silicon in bulk form, nano-sized silica particles (SiNPs) have been demonstrated to be more efficient in their beneficial roles. SiNPs can be used for various technological applications, viz. Improving soil fertility, agricultural yield, and remediating heavy metal-polluted soil. The research outcomes of studies focussing on role of silica nanoparticles to specifically mitigate the metal toxicity in plants have not been reviewed earlier in depth. The aim of this review is to explore the potential of SiNPs in alleviating metal stress and improving plant growth. The benefits of nano-silica over bulk-Si fertilizers in farming, their performance in diverse plant varieties, and the possible mechanisms to mitigate metal toxicity in plants have been discussed in detail. Further, research gaps are identified and future prospects are envisioned for advanced investigations in this field. The growing interest towards nano-silica related research will facilitate exploration of the true prospective of these nanoparticles for mitigation of metal stress in crops and in other fields of agriculture as well., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

The availability of proteomics datasets in the public domain, and in the PRIDE database, in particular, has increased dramatically in recent years. This unprecedented large-scale availability of data provides an opportunity for combined analyses of datasets to get organism-wide protein abundance data in a consistent manner. We have reanalyzed 24 public proteomics datasets from healthy human individuals to assess baseline protein abundance in 31 organs. We defined tissue as a distinct functional or structural region within an organ. Overall, the aggregated dataset contains 67 healthy tissues, corresponding to 3,119 mass spectrometry runs covering 498 samples from 489 individuals. We compared protein abundances between different organs and studied the distribution of proteins across these organs. We also compared the results with data generated in analogous studies. Additionally, we performed gene ontology and pathway-enrichment analyses to identify organ-specific enriched biological processes and pathways. As a key point, we have integrated the protein abundance results into the resource Expression Atlas, where they can be accessed and visualized either individually or together with gene expression data coming from transcriptomics datasets. We believe this is a good mechanism to make proteomics data more accessible for life scientists.

Copper(i) catalyzed alkyne azide cycloaddition (CuAAC), the quintessential example of 'click chemistry', provides an adaptable and adequate platform for the synthesis of nanogels for sustained drug release at targeted sites because of their better biocompatibility. The coupling of drugs, carried out via various synthetic routes including CuAAC, into long-chain polymeric forms like nanogels has exhibited considerable assurance in therapeutic advancements and intracellular drug delivery due to the progression of water solubility, evacuation of precocious drug release, and improved upthrust of the pharmacokinetics of the nanogels, thereby rendering them as better and efficient drug carriers. The inefficiency of drug transmission to the target areas due to the resistance of complex biological barriers in vivo is a major hurdle that impedes the therapeutic translation of nanogels. This review compiles the data of nanogels synthesized specifically via CuAAC 'click' methodology, as scaffolds for targeted drug delivery and their assimilation into nanomedicine. In addition, it elaborates the ability of CuAAC to graft specific moieties and conjugating biomolecules like proteins and growth factors, onto orthogonally functionalized polymer chains with various chemical groups resulting in nanogels that are not only more appealing but also more effective at delivering drugs, thereby enhancing their site-specific target approach and initiating selective therapies., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

The paper highlights the synergistic potential of the novel combination of Camellia sinensis (Kangra green tea) and Withania somnifera (Ashwagandha). One variable at a time approach was used to find antioxidant potential of C. sinensis and W. somnifera alone and in combination. Optimization of antioxidant potential was done by using different plant concentrations of C. sinensis and W. somnifera using a statistical approach of central composite design (CCD) of RSM (response surface methodology). Initial antioxidant activity during optimization of the solvent system was observed in methanol for C. sinensis with DPPH, superoxide radical scavenging assay and hydrogen peroxide scavenging assay (44.9 ± 0.62, 43.77 ± 0.10, 43.88 ± 0.10% scavenging) and for W. somnifera (40.22 ± 0.39, 43.29 ± 1.12, 41.88 ± 0.11% scavenging), respectively. Initially, IC 50 has been calculated for C. sinensis (235.26 ± 0.012 μg/mL) and W. somnifera (256.39 ± 0.43 μg/mL) in methanol. Before statistical optimization, the maximum synergistic antioxidant potential of C. sinensis (200 μg/mL) and W. somnifera (150 μg/mL) with DPPH assay, superoxide radical scavenging and hydrogen peroxide scavenging assay was found to be 56.57 ± 0.62, 56.99 ± 0.42, 55.44 ± 0.53% scavenging, respectively. IC 50 value has been calculated for C. sinensis  +  W. somnifera (IC 50  = 215.47 ± 0.06 μg/mL). Optimization of plant concentration using CCD of RSM resulted in enhancement of antioxidant potential of C. sinensis (200.5 μg/mL) and W. somnifera (200.5 μg/mL) was found to be 78.01 ± 0.01% scavenging when compared to the initial antioxidant potential, i.e., 56.57 ± 0.62% scavenging shows a 1.37-fold increase from initial antioxidant potential. Research unveils that using various combination of  C. sinensis and  W. somnifera enhance the antioxidant potential in vitro., Supplementary Information: The online version contains supplementary material available at 10.1007/s40011-022-01423-6., Competing Interests: Conflict of interestThe authors declare that they have no conflicts of interest., (© The Author(s), under exclusive licence to The National Academy of Sciences, India 2022. Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) is a resourceful and stereospecific methodology that has considerably yielded promising 1,2,3-triazole-appended "click" scaffolds with the potential for selective metal ion recognition. Based on "click" methodology, this report presents a chemosensor probe (TCT) based on 4- tert -butylcatechol architecture, via the CuAAC pathway, as a selective and efficient sensor for Pb(II) and Hg(II) ions, categorized as the most toxic and alarming environmental contaminants among the heavy metal ions. The synthesized probe was successfully characterized by spectroscopy [IR and NMR ( 1 H and 13 C)] and mass spectrometry. The chemosensing study performed in acetonitrile/water (4:1) solvent media, via UV-vis and fluorescence spectroscopy, established its selective sensitivity for Pb(II) and Hg(II) species among the list of explored metal ions with the limits of detection being 8.6 and 11 μM, respectively. Additionally, the 1 H NMR and IR spectra of the synthesized TCT-metal complex also confirmed the metal-ligand binding. Besides, the effect of time and temperature on the binding ability of TCT with Pb(II) and Hg(II) was also studied via UV-vis spectroscopy. Furthermore, density functional theory studies put forward the structural comprehension of the sensor by availing the hybrid density functional (B3LYP)/6311G++(d,p) basis set of theory which was subsequently utilized for investigating its anti-inflammatory potential by performing docking analysis with human leukotriene b4 protein., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

Release of untreated effluent from processing or manufacturing industries and other commercial premises into water bodies is a major threat to environment and human health. In this regard, the effluent generated from laboratories and other research facilities is of great concern. Among other harmful chemicals, the effluent is rich in toxic organic dyes, which get exposed to the environment and pose serious health risk. The dyes used in nucleic acid analysis specially the DNA dyes are known for their teratogenicity and mutagenic potential, which mainly depends upon the organism and circumstances under which it is exposed. Among animals and humans, exposure to theses dyes may lead to irritation in mouth, eyes and respiratory tract and many other possible effects which are yet to be explored. To overcome these problems, dyes present in the effluents from laboratories must be degraded to non-toxic forms. Various strategies have been proposed and investigated for degradation and remediation of contaminated laboratory effluent. As a modern and cost-effective technique, biodegradation using microbes and plants is potentially eco-friendly and sustainable technique for detoxifying these dyes. In this article, we have discussed and reviewed the structure, properties and toxicity profile of prominent nucleic acid dyes, along with the strategies of remediation of laboratory effluents contaminated with these dyes. In addition, we have also discussed the feasibility and limitations of these remediation strategies and identified research gaps that can help researchers to explore more effective solutions to manage this area of great concern. We have also reviewed various less toxic alternatives of these common as safer options of these dyes., (© 2022. Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i.)

The number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available and reproducible. To demonstrate its utility, we reanalysed 10 public DIA datasets from the PRIDE database, comprising 1,278 SWATH-MS runs. The robustness of the analysis was evaluated, and the results compared to those obtained in the original publications. The final expression values were integrated into Expression Atlas, making SWATH-MS experiments more widely available and combining them with expression data originating from other proteomics and transcriptomics datasets., (© 2022. The Author(s).)

For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae , that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

Despite many studies on the immune characteristics of Coronavirus disease 2019 (COVID-19) patients in the progression stage, a detailed understanding of pertinent immune cells in recovered patients is lacking. We performed single-cell RNA sequencing on samples from recovered COVID-19 patients and healthy controls. We created a comprehensive immune landscape with more than 260,000 peripheral blood mononuclear cells (PBMCs) from 41 samples by integrating our dataset with previously reported datasets, which included samples collected between 27 and 47 days after symptom onset. According to our large-scale single-cell analysis, recovered patients, who had severe symptoms (severe/critical recovered), still exhibited peripheral immune disorders 1-2 months after symptom onset. Specifically, in these severe/critical recovered patients, human leukocyte antigen (HLA) class II and antigen processing pathways were downregulated in both CD14 monocytes and dendritic cells compared to healthy controls, while the proportion of CD14 monocytes increased. These may lead to the downregulation of T-cell differentiation pathways in memory T cells. However, in the mild/moderate recovered patients, the proportion of plasmacytoid dendritic cells increased compared to healthy controls, accompanied by the upregulation of HLA-DRA and HLA-DRB1 in both CD14 monocytes and dendritic cells. In addition, T-cell differentiation regulation and memory T cell-related genes FOS , JUN , CD69 , CXCR4 , and CD83 were upregulated in the mild/moderate recovered patients. Further, the immunoglobulin heavy chain V3-21 ( IGHV3-21 ) gene segment was preferred in B-cell immune repertoires in severe/critical recovered patients. Collectively, we provide a large-scale single-cell atlas of the peripheral immune response in recovered COVID-19 patients., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Li, Garg, Jia, Liao, Yuan, Li, Wu, Wu, Bi, George, Papatheodorou, Brazma, Luo, Fang, Miao and Shu.)

The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets., (© 2021. The Author(s).)

Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled the genome portal's content; expanded curated genes, pathways and expression sets; and implemented the Domain Informational Vocabulary Extraction (DIVE) algorithm for extracting gene function information from publications. The current release, #63 (October 2020), hosts 93 reference genomes-over 3.9 million genes in 122 947 families with orthologous and paralogous classifications. Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of gene-gene interactions. Gramene integrates ontology-based protein structure-function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused journals using DIVE. We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome., (Published by Oxford University Press on behalf of Nucleic Acids Research 2020.)

ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data at EMBL-EBI, established in 2002, initially as an archive for publication-related microarray data and was later extended to accept sequencing-based data. Over the last decade an increasing share of biological experiments involve multiple technologies assaying different biological modalities, such as epigenetics, and RNA and protein expression, and thus the BioStudies database (https://www.ebi.ac.uk/biostudies) was established to deal with such multimodal data. Its central concept is a study, which typically is associated with a publication. BioStudies stores metadata describing the study, provides links to the relevant databases, such as European Nucleotide Archive (ENA), as well as hosts the types of data for which specialized databases do not exist. With BioStudies now fully functional, we are able to further harmonize the archival data infrastructure at EMBL-EBI, and ArrayExpress is being migrated to BioStudies. In future, all functional genomics data will be archived at BioStudies. The process will be seamless for the users, who will continue to submit data using the online tool Annotare and will be able to query and download data largely in the same manner as before. Nevertheless, some technical aspects, particularly programmatic access, will change. This update guides the users through these changes., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

The high prevalence of hypertension among African Americans makes faith-based education programs culturally appropriate. Faith-enhanced health education is a way to reach these often healthcare-disenfranchised populations. With Every Heartbeat is Life (WEHL), a community-based heart health program, was enhanced with Scripture and prayer for this project. The program took place in an African American nondenominational church. The Scripture-enhanced WEHL program emphasized biblical teachings of self-care with standard lessons on nutrition, exercise, smoking cessation, and disease management interventions that increased knowledge of hypertension and associated cardiovascular risks.

Providing quality, cost-effective care to children and their families in the appropriate setting is the goal of nurse practitioners in primary and acute care. However, increased utilization of the emergency department (ED) for nonurgent care threatens cost-effective quality care, interrupts continuity of care, and contributes to ED overcrowding. To date, descriptive research has identified demographics of those using the ED for nonurgent care, the chief complaints of children seeking nonurgent care, the cost to the health care system of pediatric nonurgent care, and characteristics of associated primary care settings. Using Donabedian's Model of Quality of Healthcare and a Theory of Dependent Care by Taylor and colleagues, acute and primary care pediatric nurse practitioners can incorporate interventions that will channel care to the appropriate setting and educate caregivers regarding common childhood illnesses and the value of continuity of care. By using a theoretical framework as a guide, this article will help both acute and primary care pediatric nurse practitioners understand why parents seek nonurgent care for their children in the ED and actions they can take to ensure that care is provided in an optimal setting., (Copyright © 2016 National Association of Pediatric Nurse Practitioners. Published by Elsevier Inc. All rights reserved.)

Degradation of residual lignin in kraft pulp by chemical bleaching is implicated in causing environmental pollution. The use of thermo- and alkali-tolerant bacterial laccases is considered to be important biological alternative to chemical processing. Laccases from Bacillus species have shown promise in this respect but their intracellular/spore bound presence make their industrial application economically unfeasible. We report here on a novel extracellular active thermo-alkali-stable laccase (SN4 laccase)  which is active at 90 °C and pH 8.0 using 2,6-dimethoxyphenol as substrate from Bacillus tequilensis SN4. SN4 laccase retained 27 % activity for 5 min at 100 °C and more than 80 % activity for 24 h at 70 °C. The enzyme is also stable at a higher pH (9.0-10.0). Enzyme production was optimized by submerged fermentation. Relatively high yields (18,356 nkats ml -1 ) of SN4 laccase was obtained in a medium containing 650 μM MnSO 4 , 350 μM FeSO 4 , and 3.5 % ethanol. A 764-fold increase in laccase activity was observed under optimal conditions. In addition, reduction in kappa number and increase in brightness of softwood pulp by 28 and 7.6 %, respectively, were observed after treatment with SN4 laccase without a mediator. When N-hydroxybenzotriazole was used as a mediator, the kappa number was decreased to 47 % and brightness was increased to 12 %.

The objective of this work was to isolate a microorganism producing alkaline protease that can be used as an ecofriendly alternative to chemicals in dehairing process of leather manufacture. Alkaline protease producing bacterium Vibrio metschnikovii NG155 was isolated from soil samples of leather industry. The protease was highly effective in dehairing of goat skin, completely eliminating the use of lime and sulfide. Histological studies of the skin after dehairing showed that the enzyme did not damage the collagen layer and brought good fiber opening. Absence of collagenase activity was confirmed by reacting pure collagen with the enzyme and analyzing it on SDS PAGE, which showed no degradation of collagen. The enzyme was stable in a wide range of pH (7-11) and temperature (10-50 °C), which makes it suitable for industrial application.

Overview: Adolescents need about nine hours of sleep per night, yet most teens get far less. Inadequate sleep has consequences not only for academic performance but also for mental and physical health; it has been linked to lowered resilience and an increased risk of cardiovascular and metabolic diseases. It's imperative that assessment of sleep become a routine part of adolescent health care. An understanding of sleep physiology is essential to helping nurses better assess and manage sleep deprivation in this population. Sleep assessment involves evaluating the three main aspects of sleep: amount, quality, and architecture. The authors provide an overview of sleep physiology, describe sleep changes that occur during adolescence, and discuss the influence of these changes on adolescent health. They also provide simple questions that nurses can use to assess sleep and risk factors for disrupted sleep, and discuss patient education and other interventions.

As home health nurses begin to more fully embrace evidence-based practice, we need to be reading research articles in addition to those being published in Home Healthcare Nurse. Many of us have been out of school for several years or have never studied nursing research, and the terminology can be daunting. Evidence-based practice strengthens our ability to provide nursing care based upon the best scientific and researched information. The evidence gleaned from research demonstrates best practice methods rather than those we have traditionally used with little or no scientific basis. The purpose of this article is to provide new knowledge or dust the cobwebs from our past studies of nursing research. A review of the types of research, as well as its language, can help home health nurses be consumers of research with greater understanding. Use of the Internet and ways to access nursing research will be discussed. This article is a brief overview only and more in-depth principles can be accessed by one of the many nursing research resources.