scholarly journals On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase

Database ◽  
2016 ◽  
Vol 2016 ◽  
Author(s):  
Hans Ienasescu ◽  
Kang Li ◽  
Robin Andersson ◽  
Morana Vitezic ◽  
Sarah Rennie ◽  
...  
Keyword(s):  
Human Body ◽  
Individual Cell ◽  
Cell Types ◽  
Large Datasets ◽  
Human Tissues ◽  
Web Tool ◽  
Expression Of Genes ◽  
Micro Rnas ◽  
Human Protein Atlas ◽  
Selection Of

Genomics consortia have produced large datasets profiling the expression of genes, micro-RNAs, enhancers and more across human tissues or cells. There is a need for intuitive tools to select subsets of such data that is the most relevant for specific studies. To this end, we present SlideBase, a web tool which offers a new way of selecting genes, promoters, enhancers and microRNAs that are preferentially expressed/used in a specified set of cells/tissues, based on the use of interactive sliders. With the help of sliders, SlideBase enables users to define custom expression thresholds for individual cell types/tissues, producing sets of genes, enhancers etc. which satisfy these constraints. Changes in slider settings result in simultaneous changes in the selected sets, updated in real time. SlideBase is linked to major databases from genomics consortia, including FANTOM, GTEx, The Human Protein Atlas and BioGPS. Database URL: http://slidebase.binf.ku.dk

scholarly journals A limited set of transcriptional programs define major cell types

2019 ◽  
Author(s):  
Alessandra Breschi ◽  
Manuel Muñoz-Aguirre ◽  
Valentin Wucher ◽  
Carrie A. Davis ◽  
Diego Garrido-Martín ◽  
...  
Keyword(s):  
Human Body ◽  
Blood Cells ◽  
Cell Types ◽  
Human Tissues ◽  
Primary Cells ◽  
Cellular Composition ◽  
Sequencing Data ◽  
Morphological Heterogeneity ◽  
Different Tissues ◽  
Age And Sex

AbstractWe have produced RNA sequencing data for a number of primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural and blood cells. These act as basic components of many tissues and organs. Based on gene expression, these cell types redefine the basic histological types by which tissues have been traditionally classified. We identified genes whose expression is specific to these cell types, and from these genes, we estimated the contribution of the major cell types to the composition of human tissues. We found this cellular composition to be a characteristic signature of tissues, and to reflect tissue morphological heterogeneity and histology. We identified changes in cellular composition in different tissues associated with age and sex and found that departures from the normal cellular composition correlate with histological phenotypes associated to disease.One Sentence SummaryA few broad transcriptional programs define the major cell types underlying the histology of human tissues and organs.

scholarly journals A single–cell type transcriptomics map of human tissues

2021 ◽  
Vol 7 (31) ◽  
pp. eabh2169
Author(s):  
Max Karlsson ◽  
Cheng Zhang ◽  
Loren Méar ◽  
Wen Zhong ◽  
Andreas Digre ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Types ◽  
Protein Profiling ◽  
Human Tissues ◽  
Cell Type ◽  
Protein Coding ◽  
Expression Of Genes ◽  
Transcriptomics Data ◽  
Single Cell Type ◽  
Resolution Single

Advances in molecular profiling have opened up the possibility to map the expression of genes in cells, tissues, and organs in the human body. Here, we combined single-cell transcriptomics analysis with spatial antibody-based protein profiling to create a high-resolution single–cell type map of human tissues. An open access atlas has been launched to allow researchers to explore the expression of human protein-coding genes in 192 individual cell type clusters. An expression specificity classification was performed to determine the number of genes elevated in each cell type, allowing comparisons with bulk transcriptomics data. The analysis highlights distinct expression clusters corresponding to cell types sharing similar functions, both within the same organs and between organs.

Microstructural comparison of synthetic bioceramics with natural bioceramics

1991 ◽  
Vol 49 ◽  
pp. 38-39
Author(s):  
Shulin Wen ◽  
Jingwei Feng ◽  
A. Krajewski ◽  
A. Ravaglioli
Keyword(s):  
Recent Work ◽  
Human Body ◽  
Human Tissues ◽  
Main Constituent ◽  
Laboratory Furnace ◽  
Chinese Adult ◽  
Human Enamel ◽  
Biological Compatibility ◽  
Synthetic Hydroxyapatite ◽  
Synthetic Work

Hydroxyapatite bioceramics has attracted many material scientists as it is the main constituent of the bone and the teeth in human body. The synthesis of the bioceramics has been performed for years. Nowadays, the synthetic work is not only focused on the hydroapatite but also on the fluorapatite and chlorapatite bioceramics since later materials have also biological compatibility with human tissues; and they may also be very promising for clinic purpose. However, in comparison of the synthetic bioceramics with natural one on microstructure, a great differences were observed according to our previous results. We have investigated these differences further in this work since they are very important to appraise the synthetic bioceramics for their clinic application.The synthetic hydroxyapatite and chlorapatite were prepared according to A. Krajewski and A. Ravaglioli and their recent work. The briquettes from different hydroxyapatite or chlorapatite powders were fired in a laboratory furnace at the temperature of 900-1300°C. The samples of human enamel selected for the comparison with synthetic bioceramics were from Chinese adult teeth.

scholarly journals Extraneous E-Cadherin Engages the Deterministic Process of Somatic Reprogramming through Modulating STAT3 and Erk1/2 Activity

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 284
Author(s):  
Yu-Hao Liu ◽  
Chien-Chang Chen ◽  
Yi-Jen Hsueh ◽  
Li-Man Hung ◽  
David Hui-Kang Ma ◽  
...  
Keyword(s):  
Stochastic Process ◽  
Molecular Mechanism ◽  
Activity Ratio ◽  
Cell Types ◽  
Deterministic Process ◽  
Modes Of Action ◽  
Molecular Events ◽  
Different Cell Types ◽  
Selection Of ◽  
E Cadherin

Although several modes of reprogramming have been reported in different cell types during iPSC induction, the molecular mechanism regarding the selection of different modes of action is still mostly unknown. The present study examined the molecular events that participate in the selection of such processes at the onset of somatic reprogramming. The activity of STAT3 versus that of Erk1/2 reversibly determines the reprogramming mode entered; a lower activity ratio favors the deterministic process and vice versa. Additionally, extraneous E-cadherin facilitates the early events of somatic reprogramming, potentially by stabilizing the LIF/gp130 and EGFR/ErbB2 complexes to promote entry into the deterministic process. Our current findings demonstrated that manipulating the pSTAT3/pErk1/2 activity ratio in the surrounding milieu can drive different modes of action toward either the deterministic or the stochastic process in the context of OSKM-mediated somatic reprogramming.

scholarly journals Diving into the Pleural Fluid: Liquid Biopsy for Metastatic Malignant Pleural Effusions

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2798
Author(s):  
Maria Alba Sorolla ◽  
Anabel Sorolla ◽  
Eva Parisi ◽  
Antonieta Salud ◽  
José M. Porcel
Keyword(s):  
Pleural Fluid ◽  
Liquid Biopsy ◽  
Cell Types ◽  
Circulating Tumor Dna ◽  
Therapeutic Interventions ◽  
Driver Mutations ◽  
Pleural Effusions ◽  
Malignant Pleural Effusions ◽  
Micro Rnas ◽  
Low Sensitivity

Liquid biopsy is emerging as a promising non-invasive diagnostic tool for malignant pleural effusions (MPE) due to the low sensitivity of conventional pleural fluid (PF) cytological examination and the difficulty to obtain tissue biopsies, which are invasive and require procedural skills. Currently, liquid biopsy is increasingly being used for the detection of driver mutations in circulating tumor DNA (ctDNA) from plasma specimens to guide therapeutic interventions. Notably, malignant PF are richer than plasma in tumor-derived products with potential clinical usefulness, such as ctDNA, micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), and circulating tumor cells (CTC). Tumor-educated cell types, such as platelets and macrophages, have also been added to this diagnostic armamentarium. Herein, we will present an overview of the role of the preceding biomarkers, collectively known as liquid biopsy, in PF samples, as well as the main technical approaches used for their detection and quantitation, including a proper sample processing. Technical limitations of current platforms and future perspectives in the field will also be addressed. Using PF as liquid biopsy shows promise for use in current practice to facilitate the diagnosis and management of metastatic MPE.

scholarly journals Dual reporter genes enabling cell tracing with viable and reliable selection of various cell types

2006 ◽  
Vol 28 (22) ◽  
pp. 1865-1865
Author(s):  
C. N. Hwang ◽  
S. Hong ◽  
S. S. Choi ◽  
K. S. Lee ◽  
S. S. Park ◽  
...  
Keyword(s):  
Reporter Genes ◽  
Cell Types ◽  
Dual Reporter ◽  
Cell Tracing ◽  
Selection Of

Pain pharmacogenetics

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Mariia A. Slepukhina ◽  
Dmitriy V. Ivashchenko ◽  
Maria A. Sheina ◽  
Andranik Alexandrovich Muradian ◽  
Dmitriy Alexeevich Blagovestnov ◽  
...  
Keyword(s):  
Literature Review ◽  
Human Body ◽  
Postoperative Analgesia ◽  
Clinical Guidelines ◽  
Original Research ◽  
General Anesthetics ◽  
Main Subject ◽  
Current Review ◽  
Inflammatory Drugs ◽  
Selection Of

AbstractPain is a significant problem in medicine. The use of PGx markers to personalize postoperative analgesia can increase its effectiveness and avoid undesirable reactions. This article describes the mechanisms of nociception and antinociception and shows the pathophysiological mechanisms of pain in the human body. The main subject of this article is pharmacogenetic approach to the selection of anesthetics. Current review presents data for local and general anesthetics, opioids, and non-steroidal anti-inflammatory drugs. None of the anesthetics currently has clinical guidelines for pharmacogenetic testing. This literature review summarizes the results of original research available, to date, and draws attention to this area.

Structural bioinformatics used to predict the protein targets of remdesivir and flavones in SARS-CoV-2 infection

2021 ◽  
Vol 17 ◽  
Author(s):  
Avram Speranta ◽  
Laura Manoliu ◽  
Catalina Sogor ◽  
Maria Mernea ◽  
Corina Duda Seiman ◽  
...  
Keyword(s):  
Human Body ◽  
Specific Treatment ◽  
Structural Similarity ◽  
Web Tool ◽  
Ligand Interaction ◽  
Protein Targets ◽  
Synthetic Compounds ◽  
Associated Proteins ◽  
Functional Features ◽  
Protein Ligand Interaction

Background: During the current SARS-CoV-2 pandemic, the identification of effective antiviral drugs is crucial. Unfortunately, no specific treatment or vaccine is available to date. Objective: Here, we aimed to predict the interactions between SARS-CoV-2 proteins and protein targets from the human body for some flavone molecules (kaempferol, morin, pectolinarin, myricitrin, and herbacetin) in comparison to synthetic compounds (hydroxychloroquine, remdesivir, ribavirin, ritonavir, AMD-070, favipiravir). Methods: Using MOE software and advanced bioinformatics and cheminformatics portals, we conducted an extensive analysis based on various structural and functional features of compounds, such as their amphiphilic field, flexibility, and steric features. The structural similarity analysis of natural and synthetic compounds was performed using Tanimoto coefficients. The interactions of some compounds with SARS-CoV-2 3CLprotease or RNA-dependent RNA polymerase were described using 2D protein-ligand interaction diagrams based on known crystal structures. The potential targets of considered compounds were identified using the SwissTargetPrediction web tool. Results: Our results showed that remdesivir, pectolinarin, and ritonavir present a strong structural similarity which may be correlated to their similar biological activity. As common molecular targets of compounds in the human body, ritonavir, kaempferol, morin, and herbacetin can activate multidrug resistance-associated proteins, while remdesivir, ribavirin, and pectolinarin appear as ligands for adenosine receptors. Conclusion: Our evaluation recommends remdesivir, pectolinarin, and ritonavir as promising anti-SARS-CoV-2 agents.

scholarly journals Micro RNAs: an arguable appraisal in medicine

2016 ◽  
Vol 50 (2) ◽  
pp. 106-124 ◽  
Author(s):  
K. Voglova ◽  
J. Bezakova ◽  
Iveta Herichova
Keyword(s):  
Clinical Trials ◽  
Human Body ◽  
Physiological State ◽  
Intercellular Signaling ◽  
Circulating Mirnas ◽  
Intracellular Space ◽  
Double Stranded Rna ◽  
Micro Rnas ◽  
Neural Diseases

AbstractMicro RNAs (miRNAs) represent a newly discovered class of regulatory molecules in the human body. miRNA is a short double stranded RNA sequence interfering with mRNA, causing in most cases, inhibition of translation. Synthesis of miRNAs shows an increasing developmental pattern and postnatally miRNAs are synthesized in all cells possessing transcriptional machinery. miRNAs usually target several mRNAs and therefore conclusive evidences proving their functions are not always ease to be acquired. In spite of this difficulty, functions of miRNAs were firmly established in the development, the cardiovascular and neural diseases, and cancer. Many miRNAs have been reported to be associated with physiological state of cells and/or tissues. This finding becomes fundamental, especially when consider that these miRNAs can be released from cell into intracellular space or circulation. Correlation between miRNA production in tissues and its contribution to multisource miRNA pool in the circulation is in a focus of biomarker-oriented researchers. Recently, circulating miRNAs have been suggested to be applicable as biomarkers in several types of cancer, cardiovascular injury, and diabetes. Role of miRNAs in the organism intercellular signaling is still under the broad investigation. Several miRNA mimics, intended for treatment of disease, are being currently tested in the clinical trials.

scholarly journals Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees

2018 ◽  
Vol 115 (8) ◽  
pp. 1854-1859 ◽  
Author(s):  
Ziheng Yang ◽  
Tianqi Zhu
Keyword(s):  
Model Selection ◽  
Bayesian Model ◽  
Phylogenetic Trees ◽  
Real Data ◽  
Bayesian Model Selection ◽  
Large Datasets ◽  
Posterior Probabilities ◽  
Misspecified Models ◽  
Full Force ◽  
Selection Of

The Bayesian method is noted to produce spuriously high posterior probabilities for phylogenetic trees in analysis of large datasets, but the precise reasons for this overconfidence are unknown. In general, the performance of Bayesian selection of misspecified models is poorly understood, even though this is of great scientific interest since models are never true in real data analysis. Here we characterize the asymptotic behavior of Bayesian model selection and show that when the competing models are equally wrong, Bayesian model selection exhibits surprising and polarized behaviors in large datasets, supporting one model with full force while rejecting the others. If one model is slightly less wrong than the other, the less wrong model will eventually win when the amount of data increases, but the method may become overconfident before it becomes reliable. We suggest that this extreme behavior may be a major factor for the spuriously high posterior probabilities for evolutionary trees. The philosophical implications of our results to the application of Bayesian model selection to evaluate opposing scientific hypotheses are yet to be explored, as are the behaviors of non-Bayesian methods in similar situations.

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