scholarly journals Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome

2021 ◽  
Vol 22 (15) ◽  
pp. 8012
Author(s):  
Rongxin Zhang ◽  
Yajun Liu ◽  
Xingxing Zhang ◽  
Ke Xiao ◽  
Yue Hou ◽  
...  
Keyword(s):  
Bioinformatics Analysis ◽  
Biological Functions ◽  
Bioinformatics Pipeline ◽  
The Real ◽  
Human Transcriptome ◽  
Gene Sets ◽  
Nucleic Acid Structures ◽  
Regulatory Functions ◽  
Whole Transcriptome ◽  
Insight Into

G-quadruplexes are the non-canonical nucleic acid structures that are preferentially formed in G-rich regions. This structure has been shown to be associated with many biological functions. Regardless of the broad efforts on DNA G-quadruplexes, we still have limited knowledge on RNA G-quadruplexes, especially in a transcriptome-wide manner. Herein, by integrating the DMS-seq and the bioinformatics pipeline, we profiled and depicted the RNA G-quadruplexes in the human transcriptome. The genes that contain RNA G-quadruplexes in their specific regions are significantly related to immune pathways and the COVID-19-related gene sets. Bioinformatics analysis reveals the potential regulatory functions of G-quadruplexes on miRNA targeting at the scale of the whole transcriptome. In addition, the G-quadruplexes are depleted in the putative, not the real, PAS-strong poly(A) sites, which may weaken the possibility of such sites being the real cleaved sites. In brief, our study provides insight into the potential function of RNA G-quadruplexes in post-transcription.

Endogenous Retroviruses Drive Resistance and Promotion of Exogenous Retroviral Homologs

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Elliott S. Chiu ◽  
Sue VandeWoude
Keyword(s):  
Immune Modulation ◽  
Viral Infections ◽  
Viral Evolution ◽  
Endogenous Retroviruses ◽  
Annual Review ◽  
Publication Date ◽  
Biological Functions ◽  
Self Tolerance ◽  
Vertebrate Hosts ◽  
Insight Into

Endogenous retroviruses (ERVs) serve as markers of ancient viral infections and provide invaluable insight into host and viral evolution. ERVs have been exapted to assist in performing basic biological functions, including placentation, immune modulation, and oncogenesis. A subset of ERVs share high nucleotide similarity to circulating horizontally transmitted exogenous retrovirus (XRV) progenitors. In these cases, ERV–XRV interactions have been documented and include ( a) recombination to result in ERV–XRV chimeras, ( b) ERV induction of immune self-tolerance to XRV antigens, ( c) ERV antigen interference with XRV receptor binding, and ( d) interactions resulting in both enhancement and restriction of XRV infections. Whereas the mechanisms governing recombination and immune self-tolerance have been partially determined, enhancement and restriction of XRV infection are virus specific and only partially understood. This review summarizes interactions between six unique ERV–XRV pairs, highlighting important ERV biological functions and potential evolutionary histories in vertebrate hosts. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Twitter content classification

First Monday ◽  
2010 ◽  
Author(s):  
Stephen Dann
Keyword(s):  
Grounded Theory ◽  
Real World ◽  
Classification Scheme ◽  
Theory Analysis ◽  
The Real ◽  
Real World Application ◽  
Classification Framework ◽  
Content Classification ◽  
Insight Into

This paper delivers a new Twitter content classification framework based sixteen existing Twitter studies and a grounded theory analysis of a personal Twitter history. It expands the existing understanding of Twitter as a multifunction tool for personal, profession, commercial and phatic communications with a split level classification scheme that offers broad categorization and specific sub categories for deeper insight into the real world application of the service.

scholarly journals Network Bioinformatics Analysis Provides Insight into Drug Repurposing for COVID-2019

2020 ◽  
Author(s):  
Xu Li ◽  
Jinchao Yu ◽  
Zhiming Zhang ◽  
Jing Ren ◽  
Alex E. Peluffo ◽  
...  
Keyword(s):  
Bioinformatics Analysis ◽  
Drug Repurposing ◽  
Clinical Settings ◽  
Clinical Knowledge ◽  
Phase 3 ◽  
Module Detection ◽  
Novel Drug ◽  
Insight Into ◽  
Old Drugs ◽  
Significant Health

The COVID-2019 disease caused by the SARS-CoV-2 virus (aka 2019-nCoV) has raised significant health concerns in China and worldwide. While novel drug discovery and vaccine studies are long, repurposing old drugs against the COVID-2019 epidemic can help identify treatments, with known preclinical, pharmacokinetic, pharmacodynamic, and toxicity profiles, which can rapidly enter Phase 3 or 4 or can be used directly in clinical settings. In this study, we presented a novel network based drug repurposing platform to identify potential drugs for the treatment of COVID-2019. We first analysed the genome sequence of SARS-CoV-2 and identified SARS as the closest disease, based on genome similarity between both causal viruses, followed by MERS and other human coronavirus diseases. Using our AutoSeed pipeline (text mining and database searches), we obtained 34 COVID-2019-related genes. Taking those genes as seeds, we automatically built a molecular network for which our module detection and drug prioritization algorithms identified 24 disease-related human pathways, five modules and finally suggested 78 drugs to repurpose. Following manual filtering based on clinical knowledge, we re-prioritized 30 potential repurposable drugs against COVID-2019 (including pseudoephedrine, andrographolide, chloroquine, abacavir, and thalidomide) . We hope that this data can provide critical insights into SARS-CoV-2 biology and help design rapid clinical trials of treatments against COVID-2019.

scholarly journals OHM’S LAW: MISCONCEPTIONS OF THE STUDENTS AT SECONDARY AND SENIOR SECONDARY LEVEL

2021 ◽  
Vol 5 (12) ◽  
Author(s):  
Yogesh Popat
Keyword(s):  
Secondary Level ◽  
The Real ◽  
Ohm’S Law ◽  
Ohm's Law ◽  
Class Room ◽  
Senior Secondary ◽  
Insight Into

The purpose of this study is to reveal the misconceptions towards the understating of ohm’s law. The sample used consists of 40 students of class X studying the Physics of CBSE curriculum. Data is collected based on essay, class room discussion and Viva-Voce. From the results of this paper it can be concluded that the students do not understands the real and actual concepts of ohm’s of by merely reading the curriculum books and by performing the experiments in school lab. The results also reflect that the misconception may also arise due to the misinterpretation of language of physics in relation to electro properly. This paper is the reflection of teaching ohm’s law in the classroom in which the students generally gets confused and develops the wrong concepts at secondary and senior secondary level. The results, discussion and conclusion in this paper will also help the teachers to develop the students’ insight into the nature of physics.

scholarly journals Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease

2020 ◽  
Author(s):  
Mary E. Dolan ◽  
David P. Hill ◽  
Gaurab Mukherjee ◽  
Monica S. McAndrews ◽  
Elissa J. Chesler ◽  
...  
Keyword(s):  
Lung Diseases ◽  
Bioinformatics Analysis ◽  
Current Knowledge ◽  
Viral Disease ◽  
Mechanisms Of Action ◽  
Biomedical Ontologies ◽  
Phenotypic Analysis ◽  
Gene Sets ◽  
Significant Enrichment ◽  
Intense Research

AbstractThe emergence of the SARS-CoV-2 virus and subsequent COVID-19 pandemic initiated intense research into the mechanisms of action for this virus. It was quickly noted that COVID-19 presents more seriously in conjunction with other human disease conditions such as hypertension, diabetes, and lung diseases. We conducted a bioinformatics analysis of COVID-19 comorbidity-associated gene sets, identifying genes and pathways shared among the comorbidities, and evaluated current knowledge about these genes and pathways as related to current information about SARS-CoV-2 infection. We performed our analysis using GeneWeaver (GW), Reactome, and several biomedical ontologies to represent and compare common COVID-19 comorbidities. Phenotypic analysis of shared genes revealed significant enrichment for immune system phenotypes and for cardiovascular-related phenotypes, which might point to alleles and phenotypes in mouse models that could be evaluated for clues to COVID-19 severity. Through pathway analysis, we identified enriched pathways shared by comorbidity datasets and datasets associated with SARS-CoV-2 infection.

scholarly journals Therapeutic Exosomes in Prognosis and Developments of Coronary Artery Disease

2021 ◽  
Vol 8 ◽  
Author(s):  
Ai-Qun Chen ◽  
Xiao-Fei Gao ◽  
Zhi-Mei Wang ◽  
Feng Wang ◽  
Shuai Luo ◽  
...  
Keyword(s):  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Cell Types ◽  
Biological Functions ◽  
Stent Restenosis ◽  
Artery Disease ◽  
Almost All ◽  
Different Cell Types ◽  
Insight Into ◽  
Systematic Knowledge

Exosomes, with an diameter of 30~150 nm, could be released from almost all types of cells, which contain diverse effective constituent, such as RNAs, proteins, lipids, and so on. In recent years, exosomes have been verified to play an important role in mechanism, diagnosis, treatment, and prognosis of cardiovascular disease, especially coronary artery disease (CAD). Moreover, it has also been shown that exosomes derived from different cell types have various biological functions based on the cell stimulation and microenvironment. However, therapeutic exosomes are currently far away from clinical translation, despite it is full of hope. In this review, we summarize an update of the recent studies and systematic knowledge of therapeutic exosomes in atherosclerosis, myocardial infarction, and in-stent restenosis, which might provide a novel insight into the treatment of CAD and promote the potential clinical application of therapeutic exosomes.

scholarly journals The Inter-α-Trypsin Inhibitor Family: Versatile Molecules in Biology and Pathology

2020 ◽  
Vol 68 (12) ◽  
pp. 907-927 ◽  
Author(s):  
Megan S. Lord ◽  
James Melrose ◽  
Anthony J. Day ◽  
John M. Whitelock
Keyword(s):  
Trypsin Inhibitor ◽  
Inhibitory Action ◽  
Family Members ◽  
Tissue Homeostasis ◽  
Protective Activity ◽  
Inflammatory Conditions ◽  
Extracellular Matrix Molecules ◽  
Chondroitin Sulfate Chain ◽  
Regulatory Functions ◽  
Insight Into

Inter-α-trypsin inhibitor (IαI) family members are ancient and unique molecules that have evolved over several hundred million years of vertebrate evolution. IαI is a complex containing the proteoglycan bikunin to which heavy chain proteins are covalently attached to the chondroitin sulfate chain. Besides its matrix protective activity through protease inhibitory action, IαI family members interact with extracellular matrix molecules and most notably hyaluronan, inhibit complement, and provide cell regulatory functions. Recent evidence for the diverse roles of the IαI family in both biology and pathology is reviewed and gives insight into their pivotal roles in tissue homeostasis. In addition, the clinical uses of these molecules are explored, such as in the treatment of inflammatory conditions including sepsis and Kawasaki disease, which has recently been associated with severe acute respiratory syndrome coronavirus 2 infection in children:

scholarly journals Does Theory Advance with Technology?

1990 ◽  
Vol 123 ◽  
pp. 409-412
Author(s):  
Halton Arp
Keyword(s):  
Cutting Edge ◽  
Extragalactic Astronomy ◽  
The Real ◽  
The Universe ◽  
Insight Into

Observational technology in astronomy moves ahead. We can see a thousand times fainter and ten to a hundred times more detail than 40 years ago. But does our application to research match the engineering progress? Most of us make the easy assumption that theory is right at the cutting edge, waiting to gobble up each new fact into an even deeper, more detailed insight into the universe. But humans frequently misunderstand the real problems and misapply technology - making everything worse for agonizingly long times.Is it possible that extragalactic astronomy has serious misconceptions? The key point to appreciate is that its whole structure rests on the belief that we know the distances to objects in the universe. The simple shift to the red of the spectrum of any observed object is assumed to measure its distance. But for 25 years evidence has been increasing that drastically incorrect distances can result. Unfortunately, not only quasar distances but the distances to the vast majority of galaxies also depend on redshifts.

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