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Article ; Online: Potential linear B-cells epitope change to a helix structure in the spike of Omicron 21L or BA.2 predicts increased SARS-CoV-2 antibodies evasion.

Al-Zyoud, Walid / Haddad, Hazem

2022 Volume 573, Page(s) 84–95

Abstract: The world health organization has announced that SARS-CoV-2 Omicron variant (B.1.1.529), including the three versions; 21K (BA.1), 21L (BA.2) and 21M (BA.3) as a variant of concern (VOC) on November 2022. In this study, we used the specialized ... ...

Abstract	The world health organization has announced that SARS-CoV-2 Omicron variant (B.1.1.529), including the three versions; 21K (BA.1), 21L (BA.2) and 21M (BA.3) as a variant of concern (VOC) on November 2022. In this study, we used the specialized computational platforms to predict the stability and flexibility of the spike protein of Omicron. The aim of this study was to investigate the expected effect of Omicron spike mutations on its physiochemical properties. Findings of this study revealed 16 stabilizing mutations that might explain a newly gained environmental stability. We expect the new mutations to play a crucial role in changing the physiochemical properties of epitopes of the spike protein. The notable finding of SuerPose work was the potential linear B-cells epitope G252 → S255 that has been changed in the spike protein of the Omicron 21L to a helix structure which might confer an escape from human monoclonal antibodies.
MeSH term(s)	Amino Acid Sequence ; Antibodies, Viral ; COVID-19 ; Epitopes, B-Lymphocyte/genetics ; Humans ; Membrane Glycoproteins/genetics ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics ; Viral Envelope Proteins/genetics
Chemical Substances	Antibodies, Viral ; Epitopes, B-Lymphocyte ; Membrane Glycoproteins ; Spike Glycoprotein, Coronavirus ; Viral Envelope Proteins ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-06-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2022.06.010
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Article: miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East

Haddad, Hazem

Abstract: MicroRNAs (miRNAs) are non-coding RNAs that control many functions within the human cells by controlling protein levels through binding to messenger RNA (mRNA) translation process or mRNA abundance. Many pieces of evidence show that miRNAs affect the ... ...

Abstract	MicroRNAs (miRNAs) are non-coding RNAs that control many functions within the human cells by controlling protein levels through binding to messenger RNA (mRNA) translation process or mRNA abundance. Many pieces of evidence show that miRNAs affect the viral RNA replication and pathogenesis through direct binding to the RNA virus to mediate changes in the host transcriptome. Many previous studies have been studying the interaction between human cells' miRNA and viral RNA to predict many targets along the viral genome. In this work, via the miRDB database, we determined the target scores of predicted human miRNA to bind with the ss-RNA of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in general and its spike gene in specific. Our predicted miRNA targets of the ss-RNA of SARS-CoV-2 might destabilize the ss-RNA translation of SARS-CoV-2 that has been established by more than 80% of asymptomatic infected cases in Jordan due to host miRNA interactions. In respiratory epithelial cells, the high prediction scoring for miRNAs covers the RNA from 5' to 3' that explains successful antiviral defenses against ss-RNA of SARS-CoV-2 and might lead to new nucleotide deletion mechanisms. The exciting findings here that the nucleotide substitution 1841Aâ¯â¯>â¯â¯G at the viral genomic RNA level, which is an amino acid substation D614G at the spike protein level showed a change in the predicted miRNA sequence from hsa-miR-4793-5p to hsa-miR-3620-3p with an increase in the target score from 91 to 92.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #32839745
Database	COVID19

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Article ; Online: Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines.

Al-Zyoud, Walid / Haddad, Hazem

Biochimie

2021 Volume 191, Page(s) 91–103

Abstract: The spike protein of SARS-CoV-2 plays a crucial role in binding with the human cell surface, which causes its pathogenicity. This study aimed to predict molecular dynamics change of emerging variants in the spike protein. In this study, several ... ...

Abstract	The spike protein of SARS-CoV-2 plays a crucial role in binding with the human cell surface, which causes its pathogenicity. This study aimed to predict molecular dynamics change of emerging variants in the spike protein. In this study, several structural biology tools, such as SuperPose, were utilized to study spike protein structures' thermodynamics, superimposition, and the spike protein disulphide bonds. This questions the current vaccines efficacies that were based on the Nextstrain clade 19A that first documented in Wuhan and lacks any variants. The prediction results of this study have exhibited the stabilizing role of the globally dominant variant, the D614G; clade 20A, and other variants in addition to their role in increasing the flexibility of the spike protein of the virus. The SuperPose findings have revealed a conformational change impact of D614G in allowing the polybasic Furin cleavage site (
MeSH term(s)	Antibodies, Neutralizing ; COVID-19/prevention & control ; COVID-19 Vaccines ; Disulfides/chemistry ; Molecular Dynamics Simulation ; Mutation ; Protein Binding ; Protein Domains ; SARS-CoV-2/chemistry ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Thermodynamics
Chemical Substances	Antibodies, Neutralizing ; COVID-19 Vaccines ; Disulfides ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-09-08
Publishing country	France
Document type	Journal Article
ZDB-ID	120345-9
ISSN	1638-6183 ; 0300-9084
ISSN (online)	1638-6183
ISSN	0300-9084
DOI	10.1016/j.biochi.2021.08.011
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Article ; Online: Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan

Walid Al-Zyoud / Hazem Haddad

Biochemistry and Biophysics Reports, Vol 25, Iss , Pp 100896- (2021)

2021

Abstract: Background: Spike protein is the surface glycoprotein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) necessary for the entry of the virus via the transmembrane receptors of the human respiratory cells causing COVID-19 disease. Aim: ... ...

Abstract	Background: Spike protein is the surface glycoprotein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) necessary for the entry of the virus via the transmembrane receptors of the human respiratory cells causing COVID-19 disease. Aim: Here, we aimed to predict the three-dimensional monomer structure of spike protein of SARS-CoV-2 from 20 Jordanian nasopharyngeal samples and to determine the percentage of single amino acid variants (SAV) in the spike protein of SARS-CoV-2. Methods: The output of the Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) found four single amino acid variants in the spike gene. Results: The first variant represented by 5% of samples that showed tyrosine deletion at Y144 located in the N terminal domain. The second and the dominant variant, represented by 62%, showed aspartate a coil amino acid substitution to glycine an extracellular amino acid at D614G located in the spike recognition binding site. The third variant, represented by 5%, showed aspartate substitution to tyrosine at D1139Y, and the fourth variant, represented by 5% glycine substitution to serine at G1167S. Conclusion: Our results have shown low mutational sensitivity in all variants except to D614G the one with the most likely neutral mutational sensitivity that all variants might not explicitly affect the function of spike glycoprotein. However, D614G might change the viral conformational plasticity and hence a potential viral fitness gain but one must be cautious about drawing any concrete conclusions about the severity of symptoms and viral transmission from genomic data only. General significance: Studying mutations such as D614G in deep is essential to control the pandemic in terms of immune systems, antibodies, or even vaccines.
Keywords	COVID-19 ; SARS-CoV-2 ; Spike ; D614G & ; Mutation ; Biology (General) ; QH301-705.5 ; Biochemistry ; QD415-436
Subject code	612
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East.

Haddad, Hazem / Walid Al-Zyoud

Non-coding RNA research

2020 Volume 5, Issue 3, Page(s) 135–143

Abstract	MicroRNAs (miRNAs) are non-coding RNAs that control many functions within the human cells by controlling protein levels through binding to messenger RNA (mRNA) translation process or mRNA abundance. Many pieces of evidence show that miRNAs affect the viral RNA replication and pathogenesis through direct binding to the RNA virus to mediate changes in the host transcriptome. Many previous studies have been studying the interaction between human cells' miRNA and viral RNA to predict many targets along the viral genome. In this work, via the miRDB database, we determined the target scores of predicted human miRNA to bind with the ss-RNA of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in general and its spike gene in specific. Our predicted miRNA targets of the ss-RNA of SARS-CoV-2 might destabilize the ss-RNA translation of SARS-CoV-2 that has been established by more than 80% of asymptomatic infected cases in Jordan due to host miRNA interactions. In respiratory epithelial cells, the high prediction scoring for miRNAs covers the RNA from 5' to 3' that explains successful antiviral defenses against ss-RNA of SARS-CoV-2 and might lead to new nucleotide deletion mechanisms. The exciting findings here that the nucleotide substitution 1841A > G at the viral genomic RNA level, which is an amino acid substation D614G at the spike protein level showed a change in the predicted miRNA sequence from hsa-miR-4793-5p to hsa-miR-3620-3p with an increase in the target score from 91 to 92.
Keywords	covid19
Language	English
Publishing date	2020-08-20
Publishing country	Netherlands
Document type	Journal Article
ISSN	2468-0540
ISSN (online)	2468-0540
DOI	10.1016/j.ncrna.2020.08.002
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan.

Al-Zyoud, Walid / Haddad, Hazem

Biochemistry and biophysics reports

2020 Volume 25, Page(s) 100896

Abstract	Background: Spike protein is the surface glycoprotein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) necessary for the entry of the virus via the transmembrane receptors of the human respiratory cells causing COVID-19 disease. Aim: Here, we aimed to predict the three-dimensional monomer structure of spike protein of SARS-CoV-2 from 20 Jordanian nasopharyngeal samples and to determine the percentage of single amino acid variants (SAV) in the spike protein of SARS-CoV-2. Methods: The output of the Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) found four single amino acid variants in the spike gene. Results: The first variant represented by 5% of samples that showed tyrosine deletion at Y144 located in the N terminal domain. The second and the dominant variant, represented by 62%, showed aspartate a coil amino acid substitution to glycine an extracellular amino acid at D614G located in the spike recognition binding site. The third variant, represented by 5%, showed aspartate substitution to tyrosine at D1139Y, and the fourth variant, represented by 5% glycine substitution to serine at G1167S. Conclusion: Our results have shown low mutational sensitivity in all variants except to D614G the one with the most likely neutral mutational sensitivity that all variants might not explicitly affect the function of spike glycoprotein. However, D614G might change the viral conformational plasticity and hence a potential viral fitness gain but one must be cautious about drawing any concrete conclusions about the severity of symptoms and viral transmission from genomic data only. General significance: Studying mutations such as D614G in deep is essential to control the pandemic in terms of immune systems, antibodies, or even vaccines.
Language	English
Publishing date	2020-12-29
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2831046-9
ISSN	2405-5808 ; 2405-5808
ISSN (online)	2405-5808
ISSN	2405-5808
DOI	10.1016/j.bbrep.2020.100896
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East

Hazem Haddad / Walid Al-Zyoud

Non-coding RNA Research, Vol 5, Iss 3, Pp 135-

2020 Volume 143

Abstract	MicroRNAs (miRNAs) are non-coding RNAs that control many functions within the human cells by controlling protein levels through binding to messenger RNA (mRNA) translation process or mRNA abundance. Many pieces of evidence show that miRNAs affect the viral RNA replication and pathogenesis through direct binding to the RNA virus to mediate changes in the host transcriptome. Many previous studies have been studying the interaction between human cells' miRNA and viral RNA to predict many targets along the viral genome. In this work, via the miRDB database, we determined the target scores of predicted human miRNA to bind with the ss-RNA of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in general and its spike gene in specific. Our predicted miRNA targets of the ss-RNA of SARS-CoV-2 might destabilize the ss-RNA translation of SARS-CoV-2 that has been established by more than 80% of asymptomatic infected cases in Jordan due to host miRNA interactions. In respiratory epithelial cells, the high prediction scoring for miRNAs covers the RNA from 5′ to 3′ that explains successful antiviral defenses against ss-RNA of SARS-CoV-2 and might lead to new nucleotide deletion mechanisms. The exciting findings here that the nucleotide substitution 1841A > G at the viral genomic RNA level, which is an amino acid substation D614G at the spike protein level showed a change in the predicted miRNA sequence from hsa-miR-4793-5p to hsa-miR-3620-3p with an increase in the target score from 91 to 92.
Keywords	miRNA ; SARS-CoV-2 ; Transmission ; Jordan ; Genetics ; QH426-470 ; covid19
Subject code	612
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	KeAi
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: MicroRNA profiling in dogs undergoing induced ischemic heart infarction: An experimental study.

Raffee, Liqaa A / Alawneh, Khaled Z / Alshehabat, Musa Ahmed Mohammed / Haddad, Hazem / Jaradat, Saied A

Veterinary world

2023 Volume 16, Issue 6, Page(s) 1319–1324

Abstract: Background and aim: MicroRNAs (miRNAs) play an important role in various biological functions. According to many studies, miRNA expression is tissue-specific, strongly controlled throughout embryogenesis, and over- or under-expressed in numerous ... ...

Abstract	Background and aim: MicroRNAs (miRNAs) play an important role in various biological functions. According to many studies, miRNA expression is tissue-specific, strongly controlled throughout embryogenesis, and over- or under-expressed in numerous disorders, including cardiovascular pathologies. This study aimed to screen, characterize, and profile many induced biomarkers (miRNAs) in dog serum before and after experimentally inducing a regional myocardial infarction (MI) by occluding the coronary arteries under general anesthesia. Materials and methods: A preclinical experimental animal study recruited 12 healthy canine dogs. The selected canine dogs were anesthetized with 1 mg/kg xylazine and 15 mg/kg ketamine before undergoing femoral arterial catheterization under fluoroscopic supervision. Commercial assay kits were used to purify total RNA and miRNA before the occlusion and 2 h after the occlusion according to the manufacturer's guidelines, and the samples were stored in RNase/DNase-free water at -80°C. Data were analyzed by GraphPad Prism 5.0 software (GraphPad Prism, San Diego, CA) SPSS, and GenEx software (www.multid.se) or (REST V3). Results: Among 325 transcribed genes, 20 were identified in 2 h. After MI, 14 biomarkers were negative, indicating downregulation, and 6 (3-F08, 3-B10, 4-A11, 1-A06, 2-E01, 3-F10) were positive, indicating upregulation. Polymerase chain reaction assay results showed a normalized fold-change in gene expression in the test sample. Fold values >1 represented a biologically significant change. Conclusion: Profiling of miRNAs before and after MI in a dog model revealed upregulation of six previously unidentified biomarkers (3-F08, 3-B10, 4-A11, 1-A06, 2-E01, and 3-F10), indicating various miRNA regulatory patterns.
Language	English
Publishing date	2023-06-13
Publishing country	India
Document type	Journal Article
ZDB-ID	2456277-4
ISSN	2231-0916 ; 0972-8988
ISSN (online)	2231-0916
ISSN	0972-8988
DOI	10.14202/vetworld.2023.1319-1324
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Potential linear B-cells epitope change to a helix structure in the spike of Omicron 21L or BA.2 predicts increased SARS-CoV-2 antibodies evasion

Al-Zyoud, Walid / Haddad, Hazem

Virology. 2022 Aug., v. 573

2022

Abstract	The world health organization has announced that SARS-CoV-2 Omicron variant (B.1.1.529), including the three versions; 21K (BA.1), 21L (BA.2) and 21M (BA.3) as a variant of concern (VOC) on November 2022. In this study, we used the specialized computational platforms to predict the stability and flexibility of the spike protein of Omicron. The aim of this study was to investigate the expected effect of Omicron spike mutations on its physiochemical properties. Findings of this study revealed 16 stabilizing mutations that might explain a newly gained environmental stability. We expect the new mutations to play a crucial role in changing the physiochemical properties of epitopes of the spike protein. The notable finding of SuerPose work was the potential linear B-cells epitope G252 → S255 that has been changed in the spike protein of the Omicron 21L to a helix structure which might confer an escape from human monoclonal antibodies.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; World Health Organization ; epitopes ; humans ; virology
Language	English
Dates of publication	2022-08
Size	p. 84-95.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2022.06.010
Database	NAL-Catalogue (AGRICOLA)

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Z 3686: Show issues

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Article ; Online: miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East

Haddad, Hazem / Walid Al-Zyoud

Non-coding RNA Research

2020 Volume 5, Issue 3, Page(s) 135–143

Keywords	covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ISSN	2468-0540
DOI	10.1016/j.ncrna.2020.08.002
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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