Bulk Assay Research Articles

Mapping cell diversity in human sporadic cerebral cavernous malformations

BackgroundCerebral cavernous malformation (CCM) is a low-flow, bleeding-prone vascular disease that can cause cerebral hemorrhage, seizure and neurological deficits. Its inheritance mode includes sporadic or autosomal dominant inheritance with incomplete penetrance, namely sporadic CCM (SCCM) and familial CCM. SCCM is featured by single lesion and single affection in a family. Among CCM patients especially SCCM, the pathogenesis of the corresponding phenotypes and pathological features or candidate genes have not been fully elucidated yet. MethodsHere, we performed in-depth single-cell RNA sequencing (scRNA-Seq) and bulk assay for transposase-accessible chromatin sequencing (ATAC-Seq) in SCCM and control patients. Further validation was conducted for the gene of interest using qPCR and RNA in situ hybridization (RNA FISH) techniques to provide further atlas and evidence for SCCM generative process. ResultsWe identified six cell types in the SCCM and control vessels and found that the expression of NEK1, RNPC3, FBRSL1, IQGAP2, MCUB, AP3B1, ESCO1, MYO9B and PVT1 were up-regulated in SCCM tissues. Among the six cell types, we found that compared with control conditions, PVT1 showed a rising peak which followed the pseudo-time axis in endothelial cell clusters of SCCM samples, while showed an increasing trend in smooth muscle cell clusters of SCCM samples. Further experiments indicated that, compared with the control vessels, PVT1 exhibited significantly elevated expression in SCCM samples. ConclusionIn SCCM conditions, We found that in the process of development from control to lesion conditions, PVT1 showed a rising peak in endothelial cells and showed an increasing trend in smooth muscle cells at the same time. Overall, there was a significantly elevated expression of NEK1, RNPC3, FBRSL1, IQGAP2, MCUB, AP3B1, ESCO1, MYO9B and PVT1 in SCCM specimens compared to control samples.

Trace element impurities in anode copper from Olympic Dam, South Australia

Anode copper is the intermediate product between copper smelting and electrorefining. Anodes are typically 98.5 to 99.8 % pure and require electrorefining to high-purity copper cathode that can be sold to customers. Impurity elements, including Ag, Au, As, Sb, Bi, Se, Te, Sn, Pb, Co, and Ni (alongside minor Fe, Al, and Si), are either dissolved within anode copper, or contained within micron-scale inclusions. To better understand the distribution of these impurities, a study of anode copper was undertaken on representative samples from the Olympic Dam anode plant, South Australia. Bulk assay for 61 elements of 269 sub-samples collected on a grid across a single anode, including the ‘ears’, shows homogeneity irrespective of location. The five most abundant impurity elements are As (mean 1279 ± 41 ppm), Se (218 ± 11 ppm), Sb (211 ± 8 ppm), Bi (202 ± 9 ppm), and Ni (195 ± 6 ppm). The assay data demonstrate that reliable, representative compositional data on the anode can be obtained from sampling and assay of only a limited part of the whole, including the ‘ears’.Trace element analysis of copper metal by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) allows quantification of dissolved minor components. Some metals, notably Ni, occur almost completely dissolved in copper. Other elements occur only partially in dissolved form, but the proportions measured in copper metal relative to bulk assay vary significantly from only ∼ 9 % for Pb, 13 % for Bi and Te, 25 % for Se, 29 % for Sn, 34 % for Sb, 55 % for As, and 60–70 % for Au, Ag, and Co. These results are consistent with the observation of a diverse suite of 1–10 µm-sized, rounded impurity inclusions containing Pb, Bi, As, Sb, Te, Se etc. that are associated with cuprite, Cu2O, and largely follow copper grain boundaries. The inclusions, each containing one or more crystalline (e.g., Cu-selenides, some Cu-Bi-arsenates, Sn-oxides and cuprite) and/or glassy phases (e.g., Cu-Pb-As-Sb-Bi-oxides), represents a trapped melt droplet, leading to the observed broad range of compositions.

Use of DNA forceps to measure receptor-ligand dissociation equilibrium constants in a single-molecule competition assay.

The ability of biophysicists to decipher the behavior of individual biomolecules has steadily improved over the past thirty years. However, it still remains unclear how an ensemble of data acquired at the single-molecule level compares with the data acquired on an ensemble of the same molecules. We here propose an assay to tackle this question in the context of dissociation equilibrium constant measurements. A sensor is built by engrafting a receptor and a ligand onto a flexible dsDNA scaffold and mounting this assembly on magnetic tweezers. This way, looking at the position of the magnetic bead enables one to determine in real-time if the two molecular partners are associated or not. Next, to quantify the affinity of the scrutinized single-receptor for a given competitor, various amounts of the latter molecule are introduced in solution and the equilibrium response of the sensor is monitored throughout the titration protocol. Proofs of concept are established for the binding of three rapamycin analogs to the FKBP12 cis-trans prolyl isomerase. For each of these drugs the mean affinity constant obtained on a ten of individual receptors agrees with the one previously determined in a bulk assay. Furthermore, experimental contingencies are sufficient to explain the dispersion observed over the single-molecule values.

Single-spore germination analyses reveal that calcium released during Clostridioides difficile germination functions in a feedforward loop.

Clostridioides difficile infections begin when its metabolically dormant spores germinate in response to sensing bile acid germinants alongside amino acid and divalent cation co-germinants in the small intestine. While bile acid germinants are essential for C. difficile spore germination, it is currently unclear whether both co-germinant signals are required. One model proposes that divalent cations, particularly Ca2+, are essential for inducing germination, while another proposes that either co-germinant class can induce germination. The former model is based on the finding that spores defective in releasing large stores of internal Ca2+ in the form of calcium dipicolinic acid (CaDPA) cannot germinate when germination is induced with bile acid germinant and amino acid co-germinant alone. However, since the reduced optical density of CaDPA-less spores makes it difficult to accurately measure their germination, we developed a novel automated, time-lapse microscopy-based germination assay to analyze CaDPA mutant germination at the single-spore level. Using this assay, we found that CaDPA mutant spores germinate in the presence of amino acid co-germinant and bile acid germinant. Higher levels of amino acid co-germinants are nevertheless required to induce CaDPA mutant spores to germinate relative to WT spores because CaDPA released by WT spores during germination can function in a feedforward loop to potentiate the germination of other spores within the population. Collectively, these data indicate that Ca2+ is not essential for inducing C. difficile spore germination because amino acid and Ca2+ co-germinant signals are sensed by parallel signaling pathways. IMPORTANCE Clostridioides difficile spore germination is essential for this major nosocomial pathogen to initiate infection. C. difficile spores germinate in response to sensing bile acid germinant signals alongside co-germinant signals. There are two classes of co-germinant signals: Ca2+ and amino acids. Prior work suggested that Ca2+ is essential for C. difficile spore germination based on bulk population analyses of germinating CaDPA mutant spores. Since these assays rely on optical density to measure spore germination and the optical density of CaDPA mutant spores is reduced relative to WT spores, this bulk assay is limited in its capacity to analyze germination. To overcome this limitation, we developed an automated image analysis pipeline to monitor C. difficile spore germination using time-lapse microscopy. With this analysis pipeline, we demonstrate that, although Ca2+ is dispensable for inducing C. difficile spore germination, CaDPA can function in a feedforward loop to potentiate the germination of neighboring spores.

FOXK1 regulates Wnt signalling to promote cardiogenesis.

Congenital heart disease (CHD) is the most common genetic birth defect, which has considerable morbidity and mortality. We focused on deciphering key regulators that govern cardiac progenitors and cardiogenesis. FOXK1 is a forkhead/winged helix transcription factor known to regulate cell cycle kinetics and is restricted to mesodermal progenitors, somites, and heart. In the present study, we define an essential role for FOXK1 during cardiovascular development. We used the mouse embryoid body system to differentiate control and Foxk1 KO embryonic stem cells into mesodermal, cardiac progenitor cells and mature cardiac cells. Using flow cytometry, immunohistochemistry, cardiac beating, transcriptional and chromatin immunoprecipitation quantitative polymerase chain reaction assays, bulk RNA sequencing (RNAseq) and assay for transposase-accessible chromatin using sequencing (ATACseq) analyses, FOXK1 was observed to be an important regulator of cardiogenesis. Flow cytometry analyses revealed perturbed cardiogenesis in Foxk1 KO embryoid bodies (EBs). Bulk RNAseq analysis at two developmental stages showed a significant reduction of the cardiac molecular program in Foxk1 KO EBs compared to the control EBs. ATACseq analysis during EB differentiation demonstrated that the chromatin landscape nearby known important regulators of cardiogenesis was significantly relaxed in control EBs compared to Foxk1 KO EBs. Furthermore, we demonstrated that in the absence of FOXK1, cardiac differentiation was markedly impaired by assaying for cardiac Troponin T expression and cardiac contractility. We demonstrate that FOXK1 is an important regulator of cardiogenesis by repressing the Wnt/β-catenin signalling pathway and thereby promoting differentiation. These results identify FOXK1 as an essential transcriptional and epigenetic regulator of cardiovascular development. Mechanistically, FOXK1 represses Wnt signalling to promote the development of cardiac progenitor cells.

Chromatin-Accessible miRNA Regulons Driving Thyroid Tumorigenesis and Progression.

Although papillary thyroid cancer can remain indolent, associated lymph node metastases and recurrence rates are approximately 50% and 20%, respectively. Omics-based medicine has led to the discovery of predictive biomarkers that can be used to predict tumor progression and clinical outcomes. We aimed to develop a noninvasive omics-driven blood test to allow accurate risk stratification and help tailor individual patient treatment plans. RNA sequencing (seq) and microRNA analysis of The Cancer Genome Atlas and Gene Expression Omnibus datasets were employed to identify an epigenetic prognostic panel. Integrated bulk assay for transposase-accessible chromatin-seq and RNA-seq experiments confirmed the results. Sixty-two paired tumor and adjacent control thyroid tissues and 67 blood samples (62 papillary thyroid cancer and 5 controls) were analyzed for validation using sequencing and real-time polymerase chain reaction and correlated to clinical outcomes. A liposome-exosome fusion clustered regularly interspaced short palindromic repeats (CRISPR)-fluorescent detection system miRNA assay was developed. A predictive risk nomogram was generated and tested for performance. Our miRNA panel (miR-146b-5p and miR-221-3p) from tissue and blood was associated with aggressive features and was located within accessible chromatin regions. The miRNA risk score and prognostic nomogram showed higher accuracy in predicting lymph node metastases (miR-146b: area under the curve [AUC] 0.816, sensitivity 76.9%; miR-221: AUC 0.740, sensitivity 79.5%) and recurrence (miR-146b: AUC 0.921, sensitivity 75.0%; miR-221: AUC 0.756, sensitivity 70.0%; p < 0.001) than staging and American Thyroid Association risk stratification. CRISPR-based miRNA assays showed upregulation in the blood of cancer cohorts. CRISPR-based detection of miR-146b and miR-221 in the blood of thyroid cancer patients is a reliable and noninvasive tool for real-time assessment and prognostication that has great potential to provide a direct impact on the care of these patients.

Biodegradable Methane Sulfonic Acid-Based Nonaqueous Dissolution, Estimation, and Recovery: Toward Development of a Simplified Scheme for Plutonium-Bearing Fuel Matrices

Designing actinide separation methodologies, which simplify process scheme and minimize radioactive waste generation, form the crux for enhancing the sustainability of the nuclear industry. The present study is a step toward development of a universal and simplified scheme for the bulk assay of plutonium and uranium as a part of chemical quality control of plutonium-bearing fuel matrices. Dissolution, estimation, and recovery form the key steps for the same. Plutonium oxide, plutonium–uranium mixed oxide, and plutonium–uranium mixed carbide were quantitatively dissolved in the biodegradable organic acid, viz., methane sulfonic acid (MSA), by heating under an infrared lamp. Usage of corrosive hydrofluoric acid or refluxing conditions were avoided. Stabilization of a single oxidation state, viz., +(IV) and +(VI) for plutonium and uranium in MSA, respectively, was confirmed by ultraviolet–visible spectrophotometry and electrometry. Electrometric studies also exhibited sharp and well separated reduction peaks for U and Pu in MSA, revealing promising possibility of simultaneous voltammetric determination of U and Pu on commercially available glassy carbon electrode. The redox energetic diffusion coefficient (D0) and heterogenous electron transfer kinetic parameters (αn and k0) of this novel system, viz., U and Pu in MSA, were obtained using cyclic voltammetry. Single stage recovery by oxalate precipitation yielding Pu removal of >98% was also demonstrated. The findings reported herein reveal the scope for prospective applications in the front end as well as back end of the nuclear fuel cycle.

Tissue registration and exploration user interfaces in support of a human reference atlas

Seventeen international consortia are collaborating on a human reference atlas (HRA), a comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. Laboratories around the world are collecting tissue specimens from donors varying in sex, age, ethnicity, and body mass index. However, harmonizing tissue data across 25 organs and more than 15 bulk and spatial single-cell assay types poses challenges. Here, we present software tools and user interfaces developed to spatially and semantically annotate (“register”) and explore the tissue data and the evolving HRA. A key part of these tools is a common coordinate framework, providing standard terminologies and data structures for describing specimen, biological structure, and spatial data linked to existing ontologies. As of April 22, 2022, the “registration” user interface has been used to harmonize and publish data on 5,909 tissue blocks collected by the Human Biomolecular Atlas Program (HuBMAP), the Stimulating Peripheral Activity to Relieve Conditions program (SPARC), the Human Cell Atlas (HCA), the Kidney Precision Medicine Project (KPMP), and the Genotype Tissue Expression project (GTEx). Further, 5,856 tissue sections were derived from 506 HuBMAP tissue blocks. The second “exploration” user interface enables consortia to evaluate data quality, explore tissue data spatially within the context of the HRA, and guide data acquisition. A companion website is at https://cns-iu.github.io/HRA-supporting-information/.

Variant allelic fraction of driver mutations predicts success of genomic methylation classification in CNS tumors.

e14035 Background: Whole genome CpG DNA methylation profiling is proving to be an extremely valuable tool in the diagnostic and prognostic classification of central nervous system (CNS) tumors, and is especially adept at discriminating between very different tumors, or tumor subtypes, that are histologically similar. However, like any bulk assay, reliability of methylation-based classification depends on sufficient tumor cellularity, as admixed nonneoplastic elements (e.g., neurons, glial cells, inflammatory cells) have their own unique methylation profiles, and thus can skew the results. Currently, it is recommended that at least 70% of the analyzed specimen be tumor; however, this is based on subjective estimates from light microscopy. Many neoplastic entities have well-known driver mutations that occur in virtually 100% of tumor cells, and next-generation sequencing (NGS) assays can detect those mutations and report their relative amounts in the form of Variant Allelic Fraction (VAF). Since NGS and methylation profiling are now frequently being done on the same tumor block, we sought to determine whether driver mutation VAF affects the accuracy of methylation profiling, and whether VAF can help establish more rigorous cutoffs for quality assurance. Methods: Using NGS and Infinium Epic850K methylation arrays, we evaluated 62 CNS neoplasms representing a range of entities, including TERT promoter-mutant glioblastoma, IDH-mutant astrocytoma, IDH-mutant oligodendroglioma, SHH-driven medulloblastoma, and CTNNB1-driven adamantinomatous craniopharyngioma. Results: VAFs of each driver mutation ranged between 1-60%. Forty-four of 62 cases (71%) had a methylation classification score ≥0.9, the most widely accepted cutoff for a successful result. A fit-of-mixture analysis via CutoffFinder (PMID: 23251644) suggested that the optimal VAF cutoff is 21%. Forty-one of 46 (89%) cases with a VAF of 21% or higher had a methylation classification score ≥0.9, whereas only 3/16 (19%) at or below 21% were classifiable with methylation profiling ( P&lt; 0.0001 by Fisher’s exact test). Nonlinear regression of VAF versus methylation score by least squares fit produced R2= 0.54, with sum of squares = 2.0. Conclusions: These data indicate that VAF can serve as a useful predictor of classification success via methylation profiling, and should be taken into account when interpreting methylation profiling results.

Ethanol Consumption Induces Nonspecific Inflammation and Functional Defects in Alveolar Macrophages.

Chronic alcohol drinking is associated with increased susceptibility to viral and bacterial respiratory pathogens. In this study, we use a rhesus macaque model of voluntary ethanol self-administration to study the effects of long-term alcohol drinking on the immunological landscape of the lung. We report a heightened inflammatory state in alveolar macrophages (AMs) obtained from ethanol (EtOH)-drinking animals that is accompanied by increased chromatin accessibility in intergenic regions that regulate inflammatory genes and contain binding motifs for transcription factors AP-1, IRF8, and NFKB p-65. In line with these transcriptional and epigenetic changes at the basal state, AMs from EtOH-drinking animals generate elevated inflammatory mediator responses to lipopolysaccharides and respiratory syncytial virus. However, the transcriptional analysis revealed an inefficient induction of interferon-stimulated genes with EtOH in response to the respiratory syncytial virus, suggesting disruption of antimicrobial defenses. Correspondingly, AMs from EtOH-drinking animals exhibited transcriptional shifts indicative of increased oxidative stress and oxidative phosphorylation, which was coupled with higher cytosolic reactive oxygen species and mitochondrial potential. This heightened oxidative stress state was accompanied by decreased ability to phagocytose bacteria. Bulk RNA and assay for transposase-accessible chromatin sequencing data further revealed reduced expression and chromatin accessibility of loci associated with tissue repair and maintenance with chronic EtOH drinking. Similarly, analysis of single-cell RNA sequencing data revealed shifts in cell states from tissue maintenance to inflammatory responses with EtOH. Collectively, these data provide novel insight into mechanisms by which chronic EtOH drinking increases susceptibility to infection in patients with alcohol use disorders.

LINEAGE: Label-free identification of endogenous informative single-cell mitochondrial RNA mutation for lineage analysis

Single-cell RNA-sequencing (scRNA-seq) has become a powerful tool for biomedical research by providing a variety of valuable information with the advancement of computational tools. Lineage analysis based on scRNA-seq provides key insights into the fate of individual cells in various systems. However, such analysis is limited by several technical challenges. On top of the considerable computational expertise and resources, these analyses also require specific types of matching data such as exogenous barcode information or bulk assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) data. To overcome these technical challenges, we developed a user-friendly computational algorithm called "LINEAGE" (label-free identification of endogenous informative single-cell mitochondrial RNA mutation for lineage analysis). Aiming to screen out endogenous markers of lineage located on mitochondrial reads from label-free scRNA-seq data to conduct lineage inference, LINEAGE integrates a marker selection strategy by feature subspace separation and de novo "low cross-entropy subspaces" identification. In this process, the mutation type and subspace-subspace "cross-entropy" of features were both taken into consideration. LINEAGE outperformed three other methods, which were designed for similar tasks as testified with two standard datasets in terms of biological accuracy and computational efficiency. Applied on a label-free scRNA-seq dataset of BRAF-mutated cancer cells, LINEAGE also revealed genes that contribute to BRAF inhibitor resistance. LINEAGE removes most of the technical hurdles of lineage analysis, which will remarkably accelerate the discovery of the important genes or cell-lineage clusters from scRNA-seq data.

Building and Using a Two-Photon Fluorescence Cross-Correlation Spectroscopy Setup Including Fluorescence Lifetime Analysis.

Fluorescence Cross-Correlation Spectroscopy (FCCS) is a well-established and useful tool in physics and chemistry. Furthermore, due to its hybrid character of being a bulk assay at a single molecular level, it found many applications in biophysics and molecular biochemistry. Examples may be investigating kinetics and dynamics of chemical and biochemical reactions suchas protein-ligand-, protein-protein-binding, fast conformational changes, and intracellular transportation. Also, it was utilized to characterize larger structures suchas lipid vesicles and multi-protein complexes. A two-photon excitation source makes FCCS relatively easy-to-use and easy-to-maintain. Combining this technique with fluorescence lifetime analysis results in a versatile biophysical tool that can be used to solve many biological problems, as even small changes in the local environment, like pH or salt concentration, can be monitored if appropriate fluorophores are used. An example of its use for membrane docking and fusion assays is described in Chap. 13 . In this chapter, we want to give the reader a simple, detailed step-by-step guideof how to set up such a tool.

Quantitative Measurement of Extracellular Vesicle Content Delivery Within Acceptor Cells.

Extracellular vesicles (EVs), including exosomes and microvesicles, are thought to transport bioactive molecules from donor to acceptor cells. Although EV uptake has been qualitatively assessed through subcellular imaging, EV content delivery has been rarely addressed due to a lack of adequate methods. Here we present a sensitive bulk assay to quantitatively measure EV uptake and content delivery in mammalian cell. In this assay, EVs containing a NanoLuc luciferase-tagged cargo are mixed with unlabeled acceptor cells. Cell fractionation separates membrane and cytosolic fractions, and luciferase activity is measured within each fraction to determine the percentage of cytosolic release. This assay can be used to further decipher cellular and molecular mechanisms that regulate the EV delivery process or to quantitatively test specific pairs of donor-acceptor cells.

The Application of Thermal Decomposition for Determination of Carbonate Acid-Neutralising Capacity for Improved Acid Mine Drainage Prediction

This study developed an industry-applicable, thermal decomposition methodology for quantification of carbonate mineral acid neutralisation capacity (ANCtherm-carb) for waste rock, tailings, and other mined materials. Standard titration-based methods for ANC can be compromised due to contributions from silicate minerals, ion exchange, Fe-rich carbonates, and other transition metal carbonates. C emission (CO2 and CO) was measured using IR in a N2 atmosphere. Cneut (wt%) was calculated using the C emission at 800 or 1000 °C minus the C emission at 400, 450 or 500 °C and the weight of sample prior to decomposition (Equation (2) of this manuscript). This value was then input into Equation (3) of this manuscript to calculate ANCtherm-carb. Good correlation of ANCtherm-carb for single-mineral carbonates with ANCcalc, calculated from bulk assay concentrations for Mg, K, Na, Ca, and Mn, was achieved. Thereafter, 18 waste rock samples were examined, resulting in the correlation of ANCtherm-carb versus non-standard ANCtitrate-carb (titration methodology adapted to focus on carbonate neutralisation only) with R2 = 0.96. This correlation is valid for samples containing both non-neutralising carbonates (siderite) and sources of neutralisation arising from non-carbonates (Mg-clay) within this waste rock system. Typically, mining operations use total C measurements for assessment of carbonate neutralisation potential in the block and mining model. This method provides an effective means to cheaply analyse for carbonate neutralisation potential with assignment of potentially acid-forming and non-acid-forming blocks to waste rock cells, etc.

High-Content Label-Free Single-Cell Analysis with a Microfluidic Device Using Programmable Scanning Electrochemical Microscopy.

The cellular heterogeneity and plasticity are often overlooked due to the averaged bulk assay in conventional methods. Optical imaging-based single-cell analysis usually requires specific labeling of target molecules inside or on the surface of the cell membrane, interfering with the physiological homeostasis of the cell. Scanning electrochemical microscopy (SECM), as an alternative approach, enables label-free imaging of single cells, which still confronts the challenge that the long-time scanning process is not feasible for large-scale analysis at the single-cell level. Herein, we developed a methodology combining a programmable SECM (P-SECM) with an addressable microwell array, which dramatically shortened the time consumption for the topography detection of the micropits array occupied by the polystyrene beads as well as the evaluation of alkaline phosphatase (ALP) activity of the 82 single cells compared with the traditional SECM imaging. This new arithmetic was based on the line scanning approach, enabling analysis of over 900 microwells within 1.2 h, which is 10 times faster than conventional SECM imaging. By implementing this configuration with the dual-mediator-based voltage-switching (VSM) mode, we investigated the activity of ALP, a promising marker for cancer stem cells, in hundreds of tumor and stromal cells on a single microwell device. The results discovered that not only a higher ALP activity is presented in cancer cells but also the heterogeneous distribution of kinetic constant (kf value) of ALP activity can be obtained at the single-cell level. By directly relating large numbers of addressed cells on the scalable microfluidic device to the deterministic routing of the above SECM tip, our platform holds potential as a high-content screening tool for label-free single-cell analysis.

A Review on process validation of solid dosage form

Objective: The purpose of this work is to perform a study on concurrent validation of levonorgestrel tablet BP 0.03mg that will deliver process validation approach as a quality assurance means. The process validation program will be investigated so that the plan will be designed to the character of the procedure under study. This can be performed by checking and controlling the various critical in process parameters.&#x0D; Method: The samples from the three consecutive batches of levonorgestrel tablet 0.03mg are collected at the different stages of the manufacturing from dispensing, mixing, granulation process, drying process, blending process, compression process. Each and every parameter are analyzed and tested as per the specifications and all the data are recorded. The obtained results must be within the specified limit range.&#x0D; Result: The results obtained from the evaluation of different parameters like bulk density, tapped density, friability, hardness, weight variation, and assay were found to be within specification limit range.&#x0D; Conclusion: The conclusion of the concurrent process validation of levonorgestrel tablet BP 0.03mg is based on the result of the validation data of three consecutive batches. It is concluded that the manufacturing process used for levonorgestrel consistently producing the stable product meeting it is predetermined specification and quality attributes.&#x0D; Keywords: Concurrent process validation, Process validation, Levonorgestrel, Critical process parameter.

The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization.

Lifelong blood production requires long-term hematopoietic stem cells (LT-HSCs), marked by stemness states involving quiescence and self-renewal, to transition into activated short-term HSCs (ST-HSCs) with reduced stemness. As few transcriptional changes underlie this transition, we used single-cell and bulk assay for transposase-accessible chromatin sequencing (ATAC-seq) on human HSCs and hematopoietic stem and progenitor cell (HSPC) subsets to uncover chromatin accessibility signatures, one including LT-HSCs (LT/HSPC signature) and another excluding LT-HSCs (activated HSPC [Act/HSPC] signature). These signatures inversely correlated during early hematopoietic commitment and differentiation. The Act/HSPC signature contains CCCTC-binding factor (CTCF) binding sites mediating 351 chromatin interactions engaged in ST-HSCs, but not LT-HSCs, enclosing multiple stemness pathway genes active in LT-HSCs and repressed in ST-HSCs. CTCF silencing derepressed stemness genes, restraining quiescent LT-HSCs from transitioning to activated ST-HSCs. Hence, 3D chromatin interactions centrally mediated by CTCF endow a gatekeeper function that governs the earliest fate transitions HSCs make by coordinating disparate stemness pathways linked to quiescence and self-renewal.

Implementation of Microfluidics for Antimicrobial Susceptibility Assays: Issues and Optimization Requirements.

Despite the continuous emergence of multi-drug resistant pathogens, the number of new antimicrobials reaching the market is critically low. Natural product peptides are a rich source of bioactive compounds, and advances in mass spectrometry have achieved unprecedented capabilities for the discovery and characterization of novel molecular species. However, traditional bioactivity assay formats hinder the discovery and biochemical characterization of natural product antimicrobial peptides (AMPs), necessitating large sample quantities and significant optimization of experimental parameters to achieve accurate/consistent activity measurements. Microfluidic devices offer a promising alternative to bulk assay systems. Herein, a microfluidics-based bioassay was compared to the traditional 96-well plate format in respective commercially-available hardware. Bioactivity in each assay type was compared using a Viola inconspicua peptide library screened against E. coli ATCC 25922. Brightfield microcopy was used to determine bioactivity in microfluidic channels while both common optical and fluorescence-based measurements of cell viability were critically assessed in plate-based assays. Exhibiting some variation in optical density and fluorescence-based measurements, all plate-based assays conferred bioactivity in late eluting V. inconspicua library fractions. However, significant differences in the bioactivity profiles of plate-based and microfluidic assays were found, and may be derived from the materials comprising each assay device or the growth/assay conditions utilized in each format. While new technologies are necessary to overcome the limitations of traditional bioactivity assays, we demonstrate that off-the-shelf implementation of microfluidic devices is non-trivial and significant method development/optimization is required before conventional use can be realized for sensitive and rapid detection of AMPs in natural product matrices.

Use of QEMSCAN® to characterize oxidized REE ore from the Bear Lodge carbonatite, Wyoming, USA

• Automated mineralogical analysis (AMA) of a complex REE deposit has characterized variations in ore types due to hydrothermal and supergene processes. • The complexity of the deposit necessitated a mineralogical survey to establish a realistic database of minerals to reference for AMA. • Resulting modes from AMA reconcile well with independent chemical assay data. • When correctly conducted, AMA provides useful data in developing mineral processing flowsheets for metallurgy, even on complex deposits with multiple ore phases. The Bear Lodge REE deposit is located in northeastern Wyoming. The Eocene carbonatite dyke and stockwork system intrudes trachytic-phonolitic rocks that contain multiple diatremes. The original magmatic characteristics of the REE-enriched carbonatite complex are strongly overprinted by carbo-hydrothermal and later supergene fluids. These fluids redistributed the REEs and created high variability in the ore mineral assemblage, as well as compositional variability within individual REE mineral species. The REE ore minerals at Bear Lodge can be classified into four types: 1. fluorocarbonates (bastnaesite, parisite, synchysite), 2. phosphates (monazite, xenotime, florencite, rhabdophane, churchite), 3. cerianite, and 4. ancylite. These minerals vary greatly in abundance, grain size, and morphology. REE distribution is heterogeneous throughout the deposit. Variations within a given REE mineral in terms of Ce depletion, Th content, degree of heavier REE enrichment, etc., create difficulties in the initial definition of discrete mineral species (i.e., by X-ray spectra) and their resultant species identification protocols for use in automated mineralogy (QEMSCAN Ⓡ in this study). Prevalent submicron-scale supergene mineralization result in hybrid spectra from multiple phases. Iterative work in reconciling QEMSCAN Ⓡ data interpretation with bulk assay, XRD, SEM, and optical petrography data allows for refinement of the protocols to quantify for both ore and gangue minerals. Use of automated mineralogy in the development of complex deposits requires rigorous review of these identification criteria in order to achieve results that can be applied with confidence to resolve mineral processing issues.

Transcriptomic, epigenetic, and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus

Neutrophil dysregulation is implicated in the pathogenesis of systemic lupus erythematosus (SLE). SLE is characterized by elevated levels of a pathogenic neutrophil subset known as low-density granulocytes (LDGs). The origin and phenotypic, functional, and pathogenic heterogeneity of LDGs remain to be systematically determined. Transcriptomics and epigenetic assessment of lupus LDGs, autologous normal-density neutrophils, and healthy control neutrophils was performed by bulk and single-cell RNA sequencing and assay for transposase-accessible chromatin sequencing. Functional readouts were compared among neutrophil subsets. SLE LDGs display significant transcriptional and epigenetic heterogeneity and comprise 2 subpopulations of intermediate-mature and immature neutrophils, with different degrees of chromatin accessibility and differences in transcription factor motif analysis. Differences in neutrophil extracellular trap (NET) formation, oxidized mitochondrial DNA release, chemotaxis, phagocytosis, degranulation, ability to harm the endothelium, and responses to type I interferon (IFN) stimulation are evident among LDG subsets. Compared with other immune cell subsets, LDGs display the highest expression of IFN-inducible genes. Distinct LDG subsets correlate with specific clinical features of lupus and with the presence and severity of coronary artery disease. Phenotypic, functional, and pathogenic neutrophil heterogeneity are prevalent in SLE and may promote immune dysregulation and prominent vascular damage characteristic of this disease.