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Chemistry of Materials : a Publication... Sep 2022The synthesis of iron oxide nanoparticles with control over size and shape has long been an area of research, with iron oleate being arguably the most successful...
The synthesis of iron oxide nanoparticles with control over size and shape has long been an area of research, with iron oleate being arguably the most successful precursor. Issues with reproducibility and versatility in iron oleate-based syntheses remain, however, in large part due to the mutable nature of its structure and stoichiometry. In this work, we characterize two new forms of iron oleate precursor that can be isolated in large quantities, show long-term stability, and have well-defined stoichiometry, leading to reproducible and predictable reactivity. Synthesis with these precursors is shown to produce iron oxide nanoparticles in a tunable size range of 4-16 nm with low size dispersity and properties consistent with magnetite in the superparamagnetic size regime.
PubMed: 36117881
DOI: 10.1021/acs.chemmater.2c02046 -
PLoS Computational Biology Oct 2019MicroRNAs are conserved, endogenous small RNAs with critical post-transcriptional regulatory functions throughout eukaryota, including prominent roles in development and...
MicroRNAs are conserved, endogenous small RNAs with critical post-transcriptional regulatory functions throughout eukaryota, including prominent roles in development and disease. Despite much effort, microRNA annotations still contain errors and are incomplete due especially to challenges related to identifying valid miRs that have small numbers of reads, to properly locating hairpin precursors and to balancing precision and recall. Here, we present miRWoods, which solves these challenges using a duplex-focused precursor detection method and stacked random forests with specialized layers to detect mature and precursor microRNAs, and has been tuned to optimize the harmonic mean of precision and recall. We trained and tuned our discovery pipeline on data sets from the well-annotated human genome, and evaluated its performance on data from mouse. Compared to existing approaches, miRWoods better identifies precursor spans, and can balance sensitivity and specificity for an overall greater prediction accuracy, recalling an average of 10% more annotated microRNAs, and correctly predicts substantially more microRNAs with only one read. We apply this method to the under-annotated genomes of Felis catus (domestic cat) and Bos taurus (cow). We identified hundreds of novel microRNAs in small RNA sequencing data sets from muscle and skin from cat, from 10 tissues from cow and also from human and mouse cells. Our novel predictions include a microRNA in an intron of tyrosine kinase 2 (TYK2) that is present in both cat and cow, as well as a family of mirtrons with two instances in the human genome. Our predictions support a more expanded miR-2284 family in the bovine genome, a larger mir-548 family in the human genome, and a larger let-7 family in the feline genome.
Topics: Animals; Base Sequence; Cats; Cattle; Computational Biology; Female; Gene Expression Regulation; Genome; High-Throughput Nucleotide Sequencing; Humans; Male; MicroRNAs; RNA Precursors; Sequence Analysis, RNA
PubMed: 31596843
DOI: 10.1371/journal.pcbi.1007309 -
Nanomaterials (Basel, Switzerland) Sep 2021This research focused on the synthesis of apatite, starting from a natural biogenic calcium source (egg-shells) and its chemical and morpho-structural characterization...
This research focused on the synthesis of apatite, starting from a natural biogenic calcium source (egg-shells) and its chemical and morpho-structural characterization in comparison with two commercial xenografts used as a bone substitute in dentistry. The synthesis route for the hydroxyapatite powder was the microwave-assisted hydrothermal technique, starting from annealed egg-shells as the precursor for lime and di-base ammonium phosphate as the phosphate precursor. The powders were characterized by Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), scanning electron microscopy (SEM), energy-dispersive X-ray analysis (EDAX), transmission electron microscopy (TEM), X-ray fluorescence spectroscopy (XRF), and cytotoxicity assay in contact with amniotic fluid stem cell (AFSC) cultures. Compositional and structural similarities or differences between the powder synthesized from egg-shells (HA1) and the two commercial xenograft powders-Bio-Oss, totally deproteinized cortical bovine bone, and Gen-Os, partially deproteinized porcine bone-were revealed. The HA1 specimen presented a single mineral phase as polycrystalline apatite with a high crystallinity (X 0.92), a crystallite size of 43.73 nm, preferential growth under the c axes (002) direction, where it mineralizes in bone, a nano-rod particle morphology, and average lengths up to 77.29 nm and diameters up to 21.74 nm. The surface of the HA1 nanoparticles and internal mesopores (mean size of 3.3 ± 1.6 nm), acquired from high-pressure hydrothermal maturation, along with the precursor's nature, could be responsible for the improved biocompatibility, biomolecule adhesion, and osteoconductive abilities in bone substitute applications. The cytotoxicity assay showed a better AFSC cell viability for HA1 powder than the commercial xenografts did, similar oxidative stress to the control sample, and improved results compared with Gen-Os. The presented preliminary biocompatibility results are promising for bone tissue regeneration applications of HA1, and the study will continue with further tests on osteoblast differentiation and mineralization.
PubMed: 34578603
DOI: 10.3390/nano11092289 -
Frontiers in Immunology 2019NK cells are generated from hematopoietic stem cells (HSC) residing in the bone marrow (BM), similar to other blood cells. Development toward mature NK cells occurs... (Review)
Review
NK cells are generated from hematopoietic stem cells (HSC) residing in the bone marrow (BM), similar to other blood cells. Development toward mature NK cells occurs largely outside the BM through travel of CD34+ and other progenitor intermediates toward secondary lymphoid organs. The BM harbors multipotent CD34+ common lymphoid progenitors (CLPs) that generate T, B, NK, and Dendritic Cells and are devoid of erythroid, myeloid, and megakaryocytic potential. Over recent years, there has been a quest for single-lineage progenitors predominantly with the objective of manipulation and intervention in mind, which has led to the identification of unipotent NK cell progenitors devoid of other lymphoid lineage potential. Research efforts for the study of lymphopoiesis have almost exclusively concentrated on healthy donor tissues and on repopulation/transplant models. This has led to the widely accepted assumption that lymphopoiesis during disease states reflects the findings of these models. However, compelling evidences in animal models show that inflammation plays a fundamental role in the regulation of HSC maturation and release in the BM niches through several mechanisms including modulation of the CXCL12-CXCR4 expression. Indeed, recent findings during systemic inflammation in patients provide evidence that a so-far overlooked CLP exists in the BM (LinCD34DNAM-1CXCR4) and that it overwhelmingly exits the BM during systemic inflammation. These "inflammatory" precursors have a developmental trajectory toward surprisingly functional NK and T cells as reviewed here and mirror the steady state maintenance of the NK cell pool by CD34DNAM-1CXCR4 precursors. Our understanding of NK cell precursor development may benefit from including a distinct "inflammatory" progenitor modeling of lymphoid precursors, allowing rapid deployment of specialized LinCD34DNAM-1CXCR4 -derived resources from the BM.
Topics: Animals; Biomarkers; Bone Marrow Cells; Cell Differentiation; Disease Susceptibility; Homeostasis; Humans; Immunophenotyping; Inflammation; Lymphoid Progenitor Cells; Stem Cell Niche
PubMed: 31555276
DOI: 10.3389/fimmu.2019.02045 -
Biochemistry Feb 2020Hedgehog proteins, a family of vital cell signaling factors, are expressed in precursor form, which requires specialized autoprocessing, called cholesterolysis, for full...
Hedgehog proteins, a family of vital cell signaling factors, are expressed in precursor form, which requires specialized autoprocessing, called cholesterolysis, for full biological activity. Cholesterolysis occurs through the action of the precursor's C-terminal enzymatic domain, HhC. In this work, we describe HhC activator compounds (HACs), a novel class of noncovalent modulators that induce autoprocessing infidelity, diminishing native cholesterolysis in favor of precursor autoproteolysis, an otherwise minor and apparently nonphysiological side reaction. HAC-induced autoproteolysis generates hedgehog protein that is cholesterol free and hence signaling deficient. The most effective HAC has an AC of 9 μM, accelerates HhC autoproteolytic activity by 225-fold, and functions in the presence and absence of cholesterol, the native substrate. HACs join a rare class of "antagonists" that suppress native enzymatic activity by subverting mechanistic fidelity.
Topics: Catalysis; Cholesterol; Drosophila Proteins; Genetic Variation; Hedgehog Proteins; Proteolysis
PubMed: 32013401
DOI: 10.1021/acs.biochem.0c00013 -
Current Neuropharmacology 2018Choline alfoscerate (α-GPC) and Cytidine 5'-diphosphocholine (CDPCholine) are both acetylcholine precursors and are considered to act as pro-cholinergic nootropic... (Review)
Review
BACKGROUND
Choline alfoscerate (α-GPC) and Cytidine 5'-diphosphocholine (CDPCholine) are both acetylcholine precursors and are considered to act as pro-cholinergic nootropic agents. Acetylcholine precursors have also recently found frequent use in the neurology clinic. Stroke and many types of dementia have been shown to respond favorably after treatment with these agents, not only in terms of cognitive dysfunction but also behavioral and psychological symptoms. The primary mechanisms of Acetylcholine precursors are the following: 1) Acetylcholine precursors themselves are used in the biosynthesis of acetylcholine and 2) byproducts like glycerophosphate have protective functions for neuronal phospholipids. However, whether acetylcholine precursors have a similar effect in treating cognitive impairment in patients with epilepsy remains controversial.
METHODS
Our previous studies investigating acetylcholine precursors in seizure-experienced animals have produced variable results that were dependent on the timing of administration.
RESULTS
Early administration of CDP-choline immediately after seizure increased neuronal death, blood-brain barrier (BBB) disruption and microglial activation in the hippocampus. However, administration of α-GPC starting 3 weeks after seizure (late administration) improved cognitive function through reduced neuronal death and BBB disruption, and increased neurogenesis in the hippocampus.
CONCLUSION
These seemingly contradictory results may be attributed to both epileptogenic features and neuroprotective functions of several acetylcholine precursors.
Topics: Animals; Cell Death; Cytidine Diphosphate Choline; Glycerylphosphorylcholine; Muscarinic Agonists; Neurons; Pilocarpine; Seizures
PubMed: 28521701
DOI: 10.2174/1570159X15666170518150053 -
Experimental Hematology Mar 2021T-Cell development is a major branch of lymphoid development and a key output of hematopoiesis, especially in early life, but the molecular requirements for T-cell... (Review)
Review
T-Cell development is a major branch of lymphoid development and a key output of hematopoiesis, especially in early life, but the molecular requirements for T-cell potential have remained obscure. Considerable advances have now been made toward solving this problem through single-cell transcriptome studies, interfaced with in vitro differentiation assays that monitor potential efficiently at the single-cell level. This review focuses on a series of recent reports studying mouse and human early T-cell precursors, both in the developing fetus and in stringently purified postnatal samples of intrathymic and prethymic T-lineage precursors. Cross-comparison of results reveals a robustly conserved core program in mouse and human, but with some informative and provocative variations between species and between ontogenic states. Repeated findings are the multipotent progenitor regulatory signature of thymus-seeding cells and the proximity of the T-cell program to dendritic cell programs, especially to plasmacytoid dendritic cells in humans.
Topics: Animals; Antigens, Differentiation, T-Lymphocyte; Cell Lineage; Cell Movement; Cell Separation; Cells, Cultured; Dendritic Cells; Fetus; Gene Expression Regulation, Developmental; Hematopoiesis; Humans; Mice; Multipotent Stem Cells; Precursor Cells, T-Lymphoid; Receptors, Antigen, T-Cell, alpha-beta; Repressor Proteins; Single-Cell Analysis; Species Specificity; Thymus Gland; Transcriptome; Tumor Suppressor Proteins
PubMed: 33454362
DOI: 10.1016/j.exphem.2020.12.005 -
Foods (Basel, Switzerland) Jun 2021Heterocyclic aromatic amines (HAAs) are potent carcinogenic compounds induced by the Maillard reaction in well-done cooked meats. Free amino acids, protein, creatinine,... (Review)
Review
Heterocyclic aromatic amines (HAAs) are potent carcinogenic compounds induced by the Maillard reaction in well-done cooked meats. Free amino acids, protein, creatinine, reducing sugars and nucleosides are major precursors involved in the production of polar and non-polar HAAs. The variety and yield of HAAs are linked with various factors such as meat type, heating time and temperature, cooking method and equipment, fresh meat storage time, raw material and additives, precursor's presence, water activity, and pH level. For the isolation and identification of HAAs, advanced chromatography and spectroscopy techniques have been employed. These potent mutagens are the etiology of several types of human cancers at the ng/g level and are 100- to 2000-fold stronger than that of aflatoxins and benzopyrene, respectively. This review summarizes previous studies on the formation and types of potent mutagenic and/or carcinogenic HAAs in cooked meats. Furthermore, occurrence, risk assessment, and factors affecting HAA formation are discussed in detail. Additionally, sample extraction procedure and quantification techniques to determine these compounds are analyzed and described. Finally, an overview is presented on the promising strategy to mitigate the risk of HAAs by natural compounds and the effect of plant extracts containing antioxidants to reduce or inhibit the formation of these carcinogenic substances in cooked meats.
PubMed: 34202792
DOI: 10.3390/foods10071466 -
Scientific Reports Jul 2018HIV-1 protease (PR) is a homodimeric enzyme that is autocatalytically cleaved from the Gag-Pol precursor. Known PR inhibitors bind the mature enzyme several orders of...
HIV-1 protease (PR) is a homodimeric enzyme that is autocatalytically cleaved from the Gag-Pol precursor. Known PR inhibitors bind the mature enzyme several orders of magnitude more strongly than the PR precursor. Inhibition of PR at the precursor level, however, may stop the process at its rate-limiting step before the proteolytic cascade is initiated. Due to its structural heterogeneity, limited solubility and autoprocessing, the PR precursor is difficult to access by classical methods, and limited knowledge regarding precursor inhibition is available. Here, we describe a cell-based assay addressing precursor inhibition. We used a reporter molecule containing the transframe (TFP) and p6* peptides, PR, and N-terminal fragment of reverse transcriptase flanked by the fluorescent proteins mCherry and EGFP on its N- and C- termini, respectively. The level of FRET between EGFP and mCherry indicates the amount of unprocessed reporter, allowing specific monitoring of precursor inhibition. The inhibition can be quantified by flow cytometry. Additionally, two microscopy techniques confirmed that the reporter remains unprocessed within individual cells upon inhibition. We tested darunavir, atazanavir and nelfinavir and their combinations against wild-type PR. Shedding light on an inhibitor's ability to act on non-mature forms of PR may aid novel strategies for next-generation drug design.
Topics: Anti-HIV Agents; Atazanavir Sulfate; Cell Line; Darunavir; Flow Cytometry; Fluorescence Resonance Energy Transfer; Fluorescent Dyes; HIV Protease Inhibitors; HIV-1; Humans; Nelfinavir; Protein Precursors; Proteolysis
PubMed: 29992979
DOI: 10.1038/s41598-018-28638-w -
Molecular Neurobiology Mar 2023A disintegrin and metalloproteinase 10 (ADAM10) plays an essential role in the regulation of survival, proliferation, migration, and differentiation of various neural...
A disintegrin and metalloproteinase 10 (ADAM10) plays an essential role in the regulation of survival, proliferation, migration, and differentiation of various neural cells. Nevertheless, the role of ADAM10 in oligodendrocyte precursors (OPCs) and myelination in the central nervous system (CNS) of developing and adult mouse brains is still unknown. We generated ADAM10 conditional knockout (ADAM10 cKO) mice lacking the ADAM10 gene primarily in OPCs by crossing NG2-Cre mice with ADAM10 mice. We found that OPCs expressed ADAM10 in the mouse corpus callosum and the hippocampus. ADAM10 cKO mice showed significant loss of back hair and reduction in weight and length on postnatal (30 ± 2.1) day, died at (65 ± 5) days after birth, and exhibited the "anxiety and depression-like" performances. Conditional knockout of ADAM10 in OPCs resulted in a prominent increase in myelination and a decrease in the number of OPCs in the corpus callosum at P30 owing to premyelination and lack of proliferation of OPCs. Moreover, the number of proliferating OPCs and mature oligodendrocytes (OLs) also decreased with age in the corpus callosum of ADAM10 cKO mice from P30 to P60. Western blot and RT-PCR results showed that the activation of Notch-1 and its four target genes, Hes1, Hes5, Hey1, and Hey2, was inhibited in the corpus callosum tissue of ADAM10 knockout mice. In our study, we provided experimental evidence to demonstrate that ADAM10 is essential for modulating CNS myelination and OPC development by activating Notch-1 signaling in the developing and adult mouse brain.
Topics: Animals; Mice; ADAM10 Protein; Amyloid Precursor Protein Secretases; Cell Differentiation; Disintegrins; Hippocampus; Membrane Proteins; Mice, Knockout; Neurogenesis; Oligodendrocyte Precursor Cells; Oligodendroglia; Corpus Callosum
PubMed: 36550333
DOI: 10.1007/s12035-022-03163-0