The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an ...atlas. However, delays between fresh sample collection and processing may lead to poor data and difficulties in experimental design.
This study assesses the effect of cold storage on fresh healthy spleen, esophagus, and lung from ≥ 5 donors over 72 h. We collect 240,000 high-quality single-cell transcriptomes with detailed cell type annotations and whole genome sequences of donors, enabling future eQTL studies. Our data provide a valuable resource for the study of these 3 organs and will allow cross-organ comparison of cell types. We see little effect of cold ischemic time on cell yield, total number of reads per cell, and other quality control metrics in any of the tissues within the first 24 h. However, we observe a decrease in the proportions of lung T cells at 72 h, higher percentage of mitochondrial reads, and increased contamination by background ambient RNA reads in the 72-h samples in the spleen, which is cell type specific.
In conclusion, we present robust protocols for tissue preservation for up to 24 h prior to scRNA-seq analysis. This greatly facilitates the logistics of sample collection for Human Cell Atlas or clinical studies since it increases the time frames for sample processing.
Elevated levels of reactive nitrogen species, alteration in redox balance and deregulated redox signaling are common hallmarks of cancer progression and chemoresistance. However, depending on the ...cellular context, distinct reactive nitrogen species are also hypothesized to mediate cytotoxic activity and are thus used in anticancer therapies. We present here the dual face of nitric oxide and its derivatives in cancer biology. Main derivatives of nitric oxide, such as nitrogen dioxide and peroxynitrite cause cell death by inducing protein and lipid peroxidation and/or DNA damage. Moreover, they control the activity of important protein players within the pro- and anti-apoptotic signaling pathways. Thus, the control of intracellular reactive nitrogen species may become a sophisticated tool in anticancer strategies.
•Nitric oxide derivatives mediate the cytotoxic effect of nitric oxide.•Post-translational modifications induced by nitric oxide derivatives regulate cancer cell death or survival.•Genotoxic effect of nitric oxide is mediated by nitric oxide derivatives.•Nitrated fatty acids as anticancer agents.•2-methoxyestradiol, metabolite of 17β-estradiol, is a intracellular inducer of nitro-oxidative stress in cancer cells.
The immune response to surgery and infection Dabrowska, Aleksandra M; Slotwinski, Robert
Central-European journal of immunology,
01/2014, Letnik:
39, Številka:
4
Journal Article
Recenzirano
Odprti dostop
Surgical trauma affects both the innate and acquired immunity. The severity of immune disorders is proportional to the extent of surgical trauma and depends on a number of factors, including ...primarily the basic disease requiring surgical treatment (e.g. cancer), often coexisting infections and impaired nutritional status. Disorder of the immune response following surgical trauma may predispose to septic complications burdened with the highest mortality rate. Extensive surgery in cancer patients is associated with simultaneous activation of pro- and anti-inflammatory processes defined as SIRS (systemic inflammatory immune response) and CARS (compensatory anti-inflammatory immune response). However, it is generally believed that major surgical trauma is accompanied by sustained postoperative immunosuppression, which is particularly important in patients operated on for cancer, since the suppression of the immune system promotes not only septic complications, but also proliferation and tumor metastasis. This paper reviews the main features of immune response to surgical trauma and possibilities of its regulation.
Bioremediation is a promising method to degrade active pharmaceutical ingredients with additional safety compared to conventional methods. This study provides the basis for a new, practical procedure ...to remove antibiotics contamination, particularly cephalosporins, spread on environmental matrix. For the experiment the fruiting bodies and their mycelia from liquid in vitro cultures of two edible species of mushrooms (Imleria badia and Lentinula edodes) were choosing because of their unique nutritional and medicinal properties and enzymatic content. The study was conducted at different time intervals by testing the possibility and speed of antibiotic mycoremediation using cefuroxime axetil in different doses. The identification of the degradation products in biomass and medium was performed on the basis of UPLC/MS analysis and supported with fragmentation patterns obtained from MS/MS experiments. Both mushroom mycelia exhibit a certain metabolic activity which causes declining cefuroxime axetil levels in the wide range of concentrations. The high removal rate (about 100% within 7 days of the experiment) is particularly effective, and could be one of the most important tools in removing soil and water pollutants.
•Mycoremediation technique to remove antibiotics contamination for environmental safety.•Evaluation the ability of fungal-based remediation to degrade cephalosporin antibiotics.•UPLC/MS/MS identification of the degradation products in biomass and medium.•Imleria badia and Lentinus edodes are efficient in waste remediation of cephalosporins.
We analysed critically the potential usefulness of RNA- and DNA-based biomarkers in supporting conventional histological diagnostic tests for prostate carcinoma (PCa) detection.
Microarray profiling ...of gene expression and DNA methylation was performed on 16 benign prostatic hyperplasia (BPH) and 32 cancerous and non-cancerous prostate samples extracted by radical prostatectomy. The predictive value of the selected biomarkers was validated by qPCR-based methods using tissue samples extracted from the 58 prostates and, separately, using 227 prostate core biopsies.
HOXC6, AMACR and PCA3 expression showed the best discrimination between PCa and BPH. All three genes were previously reported as the most promising mRNA-based markers for distinguishing cancerous lesions from benign prostate lesions; however, none were sufficiently sensitive and specific to meet the criteria for a PCa diagnostic biomarker. By contrast, DNA methylation levels of the APC, TACC2, RARB, DGKZ and HES5 promoter regions achieved high discriminating sensitivity and specificity, with area under the curve (AUCs) reaching 0.95-1.0. Only a small overlap was detected between the DNA methylation levels of PCa-positive and PCa-negative needle biopsies, with AUCs ranging between 0.854 and 0.899.
DNA methylation-based biomarkers reflect the prostate malignancy and might be useful in supporting clinical decisions for suspected PCa following an initial negative prostate biopsy.
Using dimeric dialkylgallium and dialkylindium alkoxide catalysts for the polymerization of rac -lactide ( rac -LA), we have shown for the first time that the formation of homochiral dimeric species ...Me 2 MOR 2 (M = Ga, In), induced by chiral recognition of monomeric Me 2 MOR units in the presence of Lewis base, leads to an increase of the heteroselectivity of the ring opening polymerization (ROP) of rac -LA, and therefore provides a new tool for controlling the stereoselectivity of the polymerization of heterocyclic monomers. To explain the origin of the heteroselectivity of the Me 2 Ga(μ-OCH(Me)CO 2 Me) 2 /Lewis base system in the ROP of rac -LA, structure of ( S , S )-Me 2 Ga(μ-OCH(Me)CO 2 Me) 2 (( S , S )- 1 ) and rac -Me 2 Ga(μ-OCH(Me)CO 2 Me) 2 ( 1 ) in the absence and presence of tertiary amines and pyridines was investigated. Studies were further extended by analysis of the structure/activity data for both ( S , S )-Me 2 In(μ-OCH(Me)CO 2 Me) 2 (( S , S )- 2 ) and rac -Me 2 In(μ-OCH(Me)CO 2 Me) 2 ( 2 ). Contrary to gallium complex 1 , which exists in a solution as equimolar mixture of homo- and heterochiral diastereomers, an excess of homochiral ( R *, R *)- 2 species was observed in the case of 2 . For both the Ga and In complexes, the interaction of amines with the metal center increased the tendency for the formation of homochiral species with retention of the dimeric structure in the solution. This tendency was additionally demonstrated by the structure of model dialkylgallium ( 3 ) and indium ( 4 ) complexes with monoanionic ligands possessing chiral centers in the α-position to the alkoxide oxygen and pyridine functionalities. The polymerization of rac -LA with gallium and indium catalysts ( S , S )- 1 and ( S , S )- 2 resulted in the formation of heterotactically enriched polylactide (PLA) ( P r = 0.50–0.85) and ( P r = 0.54–0.72), respectively. The heteroselectivity of the investigated systems was in line with the excess of the homochiral catalytic species. The higher activity of homochiral species activated by amines resulted in a positive non-linear effect between an excess of homochiral ( R *, R *)- 1 or ( R *, R *)- 2 catalysts and the heterotacticity of the obtained PLA. The observed dependence of stereoselectivity of rac -LA polymerization on the excess of homochiral species was similar to the asymmetric amplification in enantioselective organic catalysis; however, it is exceptional in polymerization processes.
Genome-wide mechanisms that coordinate expression of subsets of functionally related genes are largely unknown. Recent studies show that receptor tyrosine kinases and components of signal ...transduction cascades including the extracellular signal-regulated protein kinase (ERK), once thought to act predominantly in the vicinity of plasma membrane and in the cytoplasm, can be recruited to chromatin encompassing transcribed genes. Genome-wide distribution of these transducers and their relationship to transcribing RNA polymerase II (Pol2) could provide new insights about co-regulation of functionally related gene subsets. Chromatin immunoprecipitations (ChIP) followed by deep sequencing, ChIP-Seq, revealed that genome-wide binding of epidermal growth factor receptor, EGFR and ERK pathway components at EGF-responsive genes was highly correlated with characteristic mitogen-induced Pol2-profile. Endosomes play a role in intracellular trafficking of proteins including their nuclear import. Immunofluorescence revealed that EGF-activated EGFR, MEK1/2 and ERK1/2 co-localize on endosomes. Perturbation of endosome internalization process, through the depletion of AP2M1 protein, resulted in decreased number of the EGFR containing endosomes and inhibition of Pol2, EGFR/ERK recruitment to EGR1 gene. Thus, mitogen-induced co-recruitment of EGFR/ERK components to subsets of genes, a kinase module possibly pre-assembled on endosome to synchronize their nuclear import, could coordinate genome-wide transcriptional events to ensure effective cell proliferation.
The specific aim of this investigation was to study the kinetics of the degradation of cefazolin, cefaclor, cefuroxime axetil, and cefepime in aqueous solution, in the presence (or absence) of ...various redox agents (iodine solution, potassium permanganate, hydrogen peroxide, sodium thiosulfate, and ascorbic acid) as a function of temperature. Various factors, such as concentration of the analyzed compounds and redox agents, storage time, and temperature, were analyzed. The degradation process of chosen antibiotics was observed chromatographically and fitted to the kinetic models, obtaining model parameters (k, t.sub.0.1, t.sub.0.5). Principal component analysis (PCA), parallel factor analysis (PARAFAC), and hierarchical cluster analysis (HCA) methods were carried out to interpret the dependencies between these factors on the drug stability.Keywords: Cephalosporins, redox agents, degradation process, chemometrics
The cough reflex is an airway defensive process that can be modulated by afferent inputs from organs located also out of the respiratory system. A bidirectional relationship between cough and heart ...dysfunctions are presented in the article, with the special insights into an arrhythmia-triggered cough. Albeit rare, cough induced by cardiac pathologies (mainly arrhythmias) seems to be an interesting and underestimated phenomenon. This condition is usually associated with the presence of abnormal heart rhythms and ceases with successful treatment of arrhythmia either by pharmacotherapy or by radiofrequency ablation of arrhythmogenic substrate. The two main hypotheses on cough-heart relationships - reflex and hemodynamic - are discussed in the review, including the authors' perspective based on the experiences with an arrhythmia-triggered cough.
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