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Article ; Online: Intelligent system based comparative analysis study of SARS-CoV-2 spike protein and antigenic proteins in different types of vaccines.

Touati, Rabeb / Elngar, Ahmed A

Beni-Suef University journal of basic and applied sciences

2022 Volume 11, Issue 1, Page(s) 34

Abstract: Background: Coronaviruses, members of the Coronavirinae subfamily in the Coronaviridae family, are enveloped and positive-stranded RNA viruses that infect animals and humans, causing intestinal and respiratory infections. Coronavirus disease 2019 (COVID- ...

Abstract	Background: Coronaviruses, members of the Coronavirinae subfamily in the Coronaviridae family, are enveloped and positive-stranded RNA viruses that infect animals and humans, causing intestinal and respiratory infections. Coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus, named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This disease appeared, for the first time (December 2019), in China and has spread quickly worldwide causing a large number of deaths. Considering the global threat, the World Health Organization (WHO) has declared, in March 2020, COVID-19 as a pandemic. Many studies suggest the great effect of the existing vaccines to protect against symptomatic cases of death by the COVID-19 virus. This paper, proposes to compare the main antigenic proteins sequences of the existing vaccines with Spike (S) protein of the SARS-CoV-2 genome. Our choice of S protein is justified by the major role that plays it in the receptor recognition and membrane fusion process based on an intelligent system. Herein, we focus on finding a correlation between S protein and compulsory vaccines in the countries that have a less death number by COVID-19 virus. In this work, we have used a combination of coding methods, signal processing, and bioinformatic techniques with the goal to localize the similar patterns between the S gene of the SARS-Cov-2 genome and 14 investigated vaccines. Results: A total of 8 similar sequences which have a size more than 6 amino acids were identified. Further, these comparisons propose that these segments can be implicated in the immune response against COVID-19, which may explain the wide variation by country in the severity of this viral threat. Conclusions: Our in silico study suggests a possible protective effect of Poliovirus, HIB, Hepatitis B, PCV10, Measles, Mumps, and Rubella (MMR) vaccines against COVID-19.
Language	English
Publishing date	2022-03-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2768279-1
ISSN	2314-8543 ; 2314-8535 ; 2314-8543
ISSN (online)	2314-8543
ISSN	2314-8535 ; 2314-8543
DOI	10.1186/s43088-022-00216-0
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Effects of electromagnetic irrigation water treatment on soil properties and arbequina olive trees in Tunisia (Sminja, Zaghouan)

Touati, Rabeb / Laajili-Ghezal, Lamia / Nsiri, Ines / Ben Hassine, Habib / Eleuch, Ahmed / Bannour, Ahmed / Farhat, Zouhair

Communications in Soil Science and Plant Analysis. 2023 June 17, v. 54, no. 11 p.1492-1509

2023

Abstract: The scarcity of water is a major problem in Tunisia. Thus, 50% of water resources are with salinity higher than 1.5 g L⁻¹ and 16% with salinity exceeding 3 g L⁻¹. To use this saline water in crop irrigation, new technologies for water treatment can be ... ...

Abstract	The scarcity of water is a major problem in Tunisia. Thus, 50% of water resources are with salinity higher than 1.5 g L⁻¹ and 16% with salinity exceeding 3 g L⁻¹. To use this saline water in crop irrigation, new technologies for water treatment can be applied such us electromagnetic irrigation water device. In this context, a field experiment was carried out at Zitouna Agricultural Development Company in Zaghouan governorate to study the impact of magnetized irrigation water on clay soil and on leaf mineral content of Arbequina olive tree growing under drip irrigation with saline water. Bimonthly soil samples were taken with an auger every 20 cm over 1 m depth. Olive leaf samples were taken from the trees located above the soil sampling points. The results showed that soil parameters variations are the same throughout the depths 0–20, 20–40, 40–60, 60–80, and 80–100 cm. As a consequence, the interpretation of the effect of magnetized irrigation water was restricted to 0–100 cm soil depth. However, a slight decrease of the pH was observed with the use of magnetized water. On other side, we reported that the electromagnetic treatment of irrigation water increases the soil moisture (Hs) and favors the absorption of N, P, K+, and Na+ by olive tree leaf tissues. Also, water use efficiency (WUE) in the plot irrigated with treated water is equal to 1.3 compared to that irrigated with untreated water. Thus, 30% improvement in yield using treated water.
Keywords	Olea europaea ; absorption ; agricultural development ; clay soils ; field experimentation ; irrigation water ; leaves ; microirrigation ; mineral content ; olives ; pH ; plant analysis ; saline water ; salinity ; soil depth ; soil water ; water treatment ; water use efficiency ; Tunisia ; electromagnetic treatment ; soil ; Arbequina olive trees ; semi-arid region
Language	English
Dates of publication	2023-0617
Size	p. 1492-1509.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	419718-5
ISSN	1532-2416 ; 0010-3624
ISSN (online)	1532-2416
ISSN	0010-3624
DOI	10.1080/00103624.2022.2159041
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The Helitron family classification using SVM based on Fourier transform features applied on an unbalanced dataset.

Touati, Rabeb / Oueslati, Afef Elloumi / Messaoudi, Imen / Lachiri, Zied

Medical & biological engineering & computing

2019 Volume 57, Issue 10, Page(s) 2289–2304

Abstract: Helitrons are mobile sequences which belong to the class 2 of eukaryotic transposons. Their specificity resides in their mechanism of transposition: the rolling circle mechanism. They play an important role in remodeling proteomes due to their ability to ...

Abstract	Helitrons are mobile sequences which belong to the class 2 of eukaryotic transposons. Their specificity resides in their mechanism of transposition: the rolling circle mechanism. They play an important role in remodeling proteomes due to their ability to modify existing genes and introducing new ones. A major difficulty in identifying and classifying Helitron families comes from the complex structure, the unspecified length, and the unbalanced appearance number of each Helitron type. The Helitron's recognition is still not solved in literature. The purpose of this paper is to characterize and classify Helitron types using spectral features and support vector machine (SVM) classification technique. Thus, the helitronic DNA is transformed into a numerical form using the FCGS
MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Chromosomes/genetics ; Databases as Topic ; Fourier Analysis ; Genome, Helminth ; Support Vector Machine
Language	English
Publishing date	2019-08-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	282327-5
ISSN	1741-0444 ; 0025-696X ; 0140-0118
ISSN (online)	1741-0444
ISSN	0025-696X ; 0140-0118
DOI	10.1007/s11517-019-02027-5
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Article: New methodology for repetitive sequences identification in

Touati, Rabeb / Tajouri, Asma / Mesaoudi, Imen / Oueslati, Afef Elloumi / Lachiri, Zied / Kharrat, Maher

Biomedical signal processing and control

2020 Volume 64, Page(s) 102207

Abstract: Repetitive DNA sequences occupy the major proportion of DNA in the human genome and even in the other species' genomes. The importance of each repetitive DNA type depends on many factors: structural and functional roles, positions, lengths and numbers of ...

Abstract	Repetitive DNA sequences occupy the major proportion of DNA in the human genome and even in the other species' genomes. The importance of each repetitive DNA type depends on many factors: structural and functional roles, positions, lengths and numbers of these repetitions are clear examples. Conserving such DNA sequences or not in different locations in the chromosome remains a challenge for researchers in biology. Detecting their location despite their great variability and finding novel repetitive sequences remains a challenging task. To side-step this problem, we developed a new method based on signal and image processing tools. In fact, using this method we could find repetitive patterns in DNA images regardless of the repetition length. This new technique seems to be more efficient in detecting new repetitive sequences than bioinformatics tools. In fact, the classical tools present limited performances especially in case of mutations (insertion or deletion). However, modifying one or a few numbers of pixels in the image doesn't affect the global form of the repetitive pattern. As a consequence, we generated a new repetitive patterns database which contains tandem and dispersed repeated sequences. The highly repetitive sequences, we have identified in X and Y chromosomes, are shown to be located in other human chromosomes or in other genomes. The data we have generated is then taken as input to a Convolutional neural network classifier in order to classify them. The system we have constructed is efficient and gives an average of 94.4% as recognition score.
Keywords	covid19
Language	English
Publishing date	2020-10-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2241886-6
ISSN	1746-8108 ; 1746-8094
ISSN (online)	1746-8108
ISSN	1746-8094
DOI	10.1016/j.bspc.2020.102207
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Article ; Online: Classification of intra-genomic helitrons based on features extracted from different orders of FCGS

Rabeb Touati / Imen Messaoudi / Afef Elloumi Oueslati / Zied Lachiri / Maher Kharrat

Informatics in Medicine Unlocked, Vol 18, Iss , Pp - (2020)

2020

Abstract: Helitrons, eukaryotic transposable elements (TEs), were discovered 18 years ago in various genomes. In the Cænorhabditis elegans (C.elegans) genome, helitron sequences have high variability in terms of size by base pairs (bp) varied from 11 to 8965 bp ... ...

Abstract	Helitrons, eukaryotic transposable elements (TEs), were discovered 18 years ago in various genomes. In the Cænorhabditis elegans (C.elegans) genome, helitron sequences have high variability in terms of size by base pairs (bp) varied from 11 to 8965 bp from one sequence to another. These TEs are not uniformly dispersed sequences, and they have the ability to mobilize within a genome by a rolling-circle mechanism. This ability to move and reproduce in genomes enables these elements to play a major role in genomic evolution. In order to follow the evolution, we predicted helitron families (10 classes) in the C.elegans genome using the combination of the features extracted from signals corresponding to DNA sequences and the Support Vector Machine (SVM) classifier. In our classification system, the features extracted from the signals were shown to be efficient to automatically predict helitronic sequences. As a result, the Gaussian radial kernel over 100-fold cross-validation gave the best accuracy rates, ranging from 68% to 97%, with an overall mean score of 83.7%, and we successfully identified the Helitron Y1A class for a specific value of c and gamma, reaching an accuracy rate of 100%. In addition, other notable helitrons (NDNAX2, NDNAX3 Helitron_Y2) were predicted with interesting accuracy rates. Keywords: Helitrons classification, Signal, FCGS coding technique, Machine learning, SVM
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	612
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: In silico comparative study of SARS-CoV-2 proteins and antigenic proteins in BCG, OPV, MMR and other vaccines: evidence of a possible putative protective effect.

Haddad-Boubaker, Sondes / Othman, Houcemeddine / Touati, Rabeb / Ayouni, Kaouther / Lakhal, Marwa / Ben Mustapha, Imen / Ghedira, Kais / Kharrat, Maher / Triki, Henda

BMC bioinformatics

2021 Volume 22, Issue 1, Page(s) 163

Abstract: Background: Coronavirus Disease 2019 (COVID-19) is a viral pandemic disease that may induce severe pneumonia in humans. In this paper, we investigated the putative implication of 12 vaccines, including BCG, OPV and MMR in the protection against COVID-19. ...

Abstract	Background: Coronavirus Disease 2019 (COVID-19) is a viral pandemic disease that may induce severe pneumonia in humans. In this paper, we investigated the putative implication of 12 vaccines, including BCG, OPV and MMR in the protection against COVID-19. Sequences of the main antigenic proteins in the investigated vaccines and SARS-CoV-2 proteins were compared to identify similar patterns. The immunogenic effect of identified segments was, then, assessed using a combination of structural and antigenicity prediction tools. Results: A total of 14 highly similar segments were identified in the investigated vaccines. Structural and antigenicity prediction analysis showed that, among the identified patterns, three segments in Hepatitis B, Tetanus, and Measles proteins presented antigenic properties that can induce putative protective effect against COVID-19. Conclusions: Our results suggest a possible protective effect of HBV, Tetanus and Measles vaccines against COVID-19, which may explain the variation of the disease severity among regions.
MeSH term(s)	Antigens, Viral/immunology ; BCG Vaccine ; COVID-19 ; COVID-19 Vaccines ; Computer Simulation ; Cross Protection ; Humans ; Protein Conformation ; SARS-CoV-2/chemistry ; Viral Proteins/immunology ; Viral Vaccines/immunology
Chemical Substances	Antigens, Viral ; BCG Vaccine ; COVID-19 Vaccines ; Viral Proteins ; Viral Vaccines
Language	English
Publishing date	2021-03-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-021-04045-3
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Article ; Online: In silico comparative study of SARS-CoV-2 proteins and antigenic proteins in BCG, OPV, MMR and other vaccines

Sondes Haddad-Boubaker / Houcemeddine Othman / Rabeb Touati / Kaouther Ayouni / Marwa Lakhal / Imen Ben Mustapha / Kais Ghedira / Maher Kharrat / Henda Triki

BMC Bioinformatics, Vol 22, Iss 1, Pp 1-

evidence of a possible putative protective effect

2021 Volume 14

Abstract: Abstract Background Coronavirus Disease 2019 (COVID-19) is a viral pandemic disease that may induce severe pneumonia in humans. In this paper, we investigated the putative implication of 12 vaccines, including BCG, OPV and MMR in the protection against ... ...

Abstract	Abstract Background Coronavirus Disease 2019 (COVID-19) is a viral pandemic disease that may induce severe pneumonia in humans. In this paper, we investigated the putative implication of 12 vaccines, including BCG, OPV and MMR in the protection against COVID-19. Sequences of the main antigenic proteins in the investigated vaccines and SARS-CoV-2 proteins were compared to identify similar patterns. The immunogenic effect of identified segments was, then, assessed using a combination of structural and antigenicity prediction tools. Results A total of 14 highly similar segments were identified in the investigated vaccines. Structural and antigenicity prediction analysis showed that, among the identified patterns, three segments in Hepatitis B, Tetanus, and Measles proteins presented antigenic properties that can induce putative protective effect against COVID-19. Conclusions Our results suggest a possible protective effect of HBV, Tetanus and Measles vaccines against COVID-19, which may explain the variation of the disease severity among regions.
Keywords	SARS-CoV-2 ; BCG ; OPV ; MMR ; Immunogenicity ; Vaccine ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Comparative genomic signature representations of the emerging COVID-19 coronavirus and other coronaviruses: High identity and possible recombination between Bat and Pangolin coronaviruses

Touati, Rabeb / Haddad-Boubaker, Sondes / Ferchichi, Imen / Messaoudi, Imen / Ouesleti, Afef Elloumi / Triki, Henda / Lachiri, Zied / Kharrat, Maher

Genomics. 2020 Nov., v. 112, no. 6

2020

Abstract: Coronaviruses are responsible on respiratory diseases in animal and human. The combination of numerical encoding techniques and digital signal processing methods are becoming increasingly important in handling large genomic data. In this paper, we ... ...

Abstract	Coronaviruses are responsible on respiratory diseases in animal and human. The combination of numerical encoding techniques and digital signal processing methods are becoming increasingly important in handling large genomic data. In this paper, we propose to analyze the SARS-CoV-2 genomic signature using the combination of different nucleotide representations and signal processing tools in the aim to identify its genetic origin. The sequence of SARS-CoV-2 was compared with 21 relevant sequences including Bat, Yak and Pangolin coronavirus sequences. In addition, we developed a new algorithm to locate the nucleotide modifications. The results show that the Bat and Pangolin coronaviruses were the most related to SARS-CoV-2 with 96% and 86% of identity all along the genome. Within the S gene sequence, the Pangolin sequence presents local highest nucleotide identity. Those findings suggest genesis of SARS-Cov-2 through evolution from Bat and Pangolin strains. This study offers new ways to automatically characterize viruses.
Keywords	Severe acute respiratory syndrome coronavirus 2 ; algorithms ; genome ; genomics ; humans ; nucleotide sequences ; processing technology ; respiratory tract diseases ; yaks
Language	English
Dates of publication	2020-11
Size	p. 4189-4202.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2020.07.003
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Article ; Online: Comparative genomic signature representations of the emerging COVID-19 coronavirus and other coronaviruses: High identity and possible recombination between Bat and Pangolin coronaviruses.

Touati, Rabeb / Haddad-Boubaker, Sondes / Ferchichi, Imen / Messaoudi, Imen / Ouesleti, Afef Elloumi / Triki, Henda / Lachiri, Zied / Kharrat, Maher

Genomics

2020 Volume 112, Issue 6, Page(s) 4189–4202

Abstract	Coronaviruses are responsible on respiratory diseases in animal and human. The combination of numerical encoding techniques and digital signal processing methods are becoming increasingly important in handling large genomic data. In this paper, we propose to analyze the SARS-CoV-2 genomic signature using the combination of different nucleotide representations and signal processing tools in the aim to identify its genetic origin. The sequence of SARS-CoV-2 was compared with 21 relevant sequences including Bat, Yak and Pangolin coronavirus sequences. In addition, we developed a new algorithm to locate the nucleotide modifications. The results show that the Bat and Pangolin coronaviruses were the most related to SARS-CoV-2 with 96% and 86% of identity all along the genome. Within the S gene sequence, the Pangolin sequence presents local highest nucleotide identity. Those findings suggest genesis of SARS-Cov-2 through evolution from Bat and Pangolin strains. This study offers new ways to automatically characterize viruses.
MeSH term(s)	Algorithms ; Animals ; Chiroptera/virology ; Coronavirus/genetics ; Genome, Viral/genetics ; Genomics/methods ; Humans ; Pangolins/virology ; Recombination, Genetic ; SARS-CoV-2/genetics
Keywords	covid19
Language	English
Publishing date	2020-07-06
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2020.07.003
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Article ; Online: Comparative genomic signature representations of the emerging COVID-19 coronavirus and other coronaviruses

Touati, Rabeb / Haddad-Boubaker, Sondes / Ferchichi, Imen / Messaoudi, Imen / Ouesleti, Afef Elloumi / Triki, Henda / Lachiri, Zied / Kharrat, Maher

Genomics

High identity and possible recombination between Bat and Pangolin coronaviruses

2020 Volume 112, Issue 6, Page(s) 4189–4202

Keywords	Genetics ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2020.07.003
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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