Full professor at Centre de Biotechnologie de Sfax, Tunisia. Director of research lab and expert in computational biology. Published over 200 papers in peer reviewed journals. Member of several international expert committees and journal editorial boards.
Food security will be affected by climate change worldwide, particularly in the developing world,... more Food security will be affected by climate change worldwide, particularly in the developing world, where the most important food products originate from plants. Plants are often exposed to environmental stresses that may affect their growth, development, yield, and food quality. Auxin is a hormone that plays a critical role in improving plants’ tolerance of environmental conditions. Auxin controls the expression of many stress-responsive genes in plants by interacting with specific cis-regulatory elements called auxin-responsive elements (AuxREs). In this work, we performed an in silico prediction of AuxREs in promoters of five auxin-responsive genes in Zea mays. We applied a data fusion approach based on the combined use of Dempster-Shafer evidence theory and fuzzy sets. Auxin has a direct impact on cell membrane proteins. The short-term auxin response may be represented by the regulation of transmembrane gene expression. The detection of an AuxRE in the promoter of prolyl oligopept...
Quinoa constitutes among the tolerant plants to the challenging and harmful abiotic environmental... more Quinoa constitutes among the tolerant plants to the challenging and harmful abiotic environmental factors. Quinoa was selected as among the model crops destined for bio-saline agriculture that could contribute to the staple food security for an ever-growing worldwide population under various climate change scenarios. The auxin response factors (ARFs) constitute the main contributors in the plant adaptation to severe environmental conditions. Thus, the determination of the ARF-binding sites represents the major step that could provide promising insights helping in plant breeding programs and improving agronomic traits. Hence, determining the ARF-binding sites is a challenging task, particularly in species with large genome sizes. In this report, we present a data fusion approach based on Dempster–Shafer evidence theory and fuzzy set theory to predict the ARF-binding sites. We then performed an “In-silico” identification of the ARF-binding sites in Chenopodium quinoa. The characteriza...
The coronary artery disease (CAD) is a chronic inflammatory disease involving genetic as well as ... more The coronary artery disease (CAD) is a chronic inflammatory disease involving genetic as well as environmental factors. Recent evidence suggests that the oral microbiome has a significant role in triggering atherosclerosis. The present study assessed the oral microbiome composition variation between coronary patients and healthy subjects in order to identify a potential pathogenic signature associated with CAD. We performed metagenomic profiling of salivary microbiomes by 16S ribosomal RNA (rRNA) next-generation sequencing. Oral microbiota profiling was performed for 30 individuals including 20 patients with CAD and ten healthy individuals without carotid plaques or previous stroke or myocardial infarction. We found that oral microbial communities in patients and healthy controls are represented by similar global core oral microbiome. The predominant taxa belonged to Firmicutes (genus Streptococcus, Veillonella, Granulicatella, Selenomonas), Proteobacteria (genus Neisseria, Haemophi...
The WRKY transcription factors superfamily are involved in diverse biological processes in plants... more The WRKY transcription factors superfamily are involved in diverse biological processes in plants including response to biotic and abiotic stresses and plant immunity. Protein-protein interaction network is a useful approach for understanding these complex processes. The availability of Arabidopsis Thaliana interactome offers a good opportunity to do get a global view of protein network. In this work, we have constructed the WRKY transcription factor network by combining different sources of evidence and we characterized its topological features using computational tools. We found that WRKY network is a hub-based network involving multifunctional proteins denoted as hubs such as WRKY 70, WRKY40, WRKY 53, WRKY 60, WRKY 33 and WRKY 51. Functional annotation showed seven functional modules particularly involved in biotic stress and defense responses. Furthermore, the gene ontology and pathway enrichment analysis revealed that WRKY proteins are mainly involved in plant-pathogen interact...
Results regarding the origin and domestication steps of almond and its dissemination around the M... more Results regarding the origin and domestication steps of almond and its dissemination around the Mediterranean basin are very controversial. The general belief is that the domestication was in the eastern side and then its dissemination to the western part was through the different trade routes. A recent study has proved using a combination of nuclear and chloroplast microsatellites a westward dispersal of almond and a long-standing presence of domesticated almond in northern Africa. In order to contribute to this discussion, new interpretation of the previous study using 10 SSRs to analyse 82 almond accessions from different origins was undertaken. The dendogram based on the similarity matrix presented four main clusters. In group A were present the majority of the local genotypes that originate from the centre and the south. Contrarily, all cultivars from the north were in group C and clustered with the European and American genotypes. In fact, the Bayesian-based analysis endorses ...
Olive tree (Olea europaea L.) is mainly grown in the Mediterranean area, which is the most import... more Olive tree (Olea europaea L.) is mainly grown in the Mediterranean area, which is the most important oil-producing crop. In spite of its cultural, economic and nutritional importance, numerous DNA markers accomplished to compositional analyzes by bioinformatic tools have been used to illustrate and reveal homonyms, synonyms and unknown accessions. The objectives of this study were (1) to analyze 5 SNP and 8 SSR markers to characterize 12 olive genotypes originating from different regions of Tunisia and (2) to resolve the denomination ambiguity of Zalmati and Chemlali Tataouine cultivars. Analyses indicated the presence of two erroneous denominations of cultivars.
SARS-CoV-2 across Africa The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-... more SARS-CoV-2 across Africa The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been hard to track in African countries, largely because of patchy data. Wilkinson et al . curated viral genomes collected in 2021 from several countries across the continent. Outbreaks during 2020 in each African country were initiated by imported cases, mostly from Europe. As the pandemic developed, case numbers in African countries were likely many times higher than reported, and subsequent waves of the pandemic appear to have been more severe. Consequently, high-transmission variants have emerged that have spread within the continent, and African countries must be included in global control efforts. —CA
B7-H6 and PD-L1 belong to the B7 family co-stimulatory molecules fine-tuning the immune response.... more B7-H6 and PD-L1 belong to the B7 family co-stimulatory molecules fine-tuning the immune response. The present work investigates the clinical effect of B7-H6 protein expression with PD-L1 status and the infiltration of natural killer cells as potential biomarkers in breast tumor inflammatory microenvironment. The expression levels of B7-H6 protein by cancer cells and immune infiltrating cells in human breast cancer tissues and evaluate their associations with PD-L1 expression, NK cell status, clinical pathological features and prognosis were explored. The immunohistochemistry labeling method was used to assess B7-H6 and PD-L1 proteins expression by cancer and immune cells. The associations between immune checkpoint, major clinical pathological variables and survival rates were analyzed. B7-H6 protein was depicted in both breast and immune cells. Results showed that Tumor B7-H6 expression is highly associated with Her-2 over expression. B7-H6 + immune cells are highly related to the S...
This is the first work performed in the shellfish production area located along the Sfax coasts (... more This is the first work performed in the shellfish production area located along the Sfax coasts (southern Tunisia) on the spatial and temporal patterns of toxic phytoplankton. It relates the excessive introduction of phosphorus in coastal waters from sediments contaminated with that nutrient. A multivariate approach was applyed using data derived from the National Phytoplankton Monitoring Program (REPHY) (2006-2009). We also examine if there is a direct relationship between the abundance of toxic phytoplankton and physical and chemical parameters. This study is based on phytoplankton composition and abundance, as well as physical and chemical data to evaluate the ecological status of the Sfax coasts, at shellfish farms. A total of 13 taxa included in the Intergovernmental Oceanographic Commission (IOC) toxic algae checklist and well-known bloom formers were identified in REPHY. Higher nutrient spring samples were distinguished from those of lower nutrient summer waters. The Redundan...
Auxin is a major regulator of plant growth and development; its action involves transcriptional a... more Auxin is a major regulator of plant growth and development; its action involves transcriptional activation. The identification of Auxin-response element (AuxRE) is one of the most important issues to understand the Auxin regulation of gene expression. Over the past few years, a large number of motif identification tools have been developed. Despite these considerable efforts provided by computational biologists, building reliable models to predict regulatory elements has still been a difficult challenge. In this context, we propose in this work a data fusion approach for the prediction of AuxRE. Our method is based on the combined use of Dempster-Shafer evidence theory and fuzzy theory. To evaluate our model, we have scanning the DORNRÖSCHEN promoter by our model. All proven AuxRE present in the promoter has been detected. At the 0.9 threshold we have no false positive. The comparison of the results of our model and some previous motifs finding tools shows that our model can predict...
Food security will be affected by climate change worldwide, particularly in the developing world,... more Food security will be affected by climate change worldwide, particularly in the developing world, where the most important food products originate from plants. Plants are often exposed to environmental stresses that may affect their growth, development, yield, and food quality. Auxin is a hormone that plays a critical role in improving plants’ tolerance of environmental conditions. Auxin controls the expression of many stress-responsive genes in plants by interacting with specific cis-regulatory elements called auxin-responsive elements (AuxREs). In this work, we performed an in silico prediction of AuxREs in promoters of five auxin-responsive genes in Zea mays. We applied a data fusion approach based on the combined use of Dempster-Shafer evidence theory and fuzzy sets. Auxin has a direct impact on cell membrane proteins. The short-term auxin response may be represented by the regulation of transmembrane gene expression. The detection of an AuxRE in the promoter of prolyl oligopept...
Quinoa constitutes among the tolerant plants to the challenging and harmful abiotic environmental... more Quinoa constitutes among the tolerant plants to the challenging and harmful abiotic environmental factors. Quinoa was selected as among the model crops destined for bio-saline agriculture that could contribute to the staple food security for an ever-growing worldwide population under various climate change scenarios. The auxin response factors (ARFs) constitute the main contributors in the plant adaptation to severe environmental conditions. Thus, the determination of the ARF-binding sites represents the major step that could provide promising insights helping in plant breeding programs and improving agronomic traits. Hence, determining the ARF-binding sites is a challenging task, particularly in species with large genome sizes. In this report, we present a data fusion approach based on Dempster–Shafer evidence theory and fuzzy set theory to predict the ARF-binding sites. We then performed an “In-silico” identification of the ARF-binding sites in Chenopodium quinoa. The characteriza...
The coronary artery disease (CAD) is a chronic inflammatory disease involving genetic as well as ... more The coronary artery disease (CAD) is a chronic inflammatory disease involving genetic as well as environmental factors. Recent evidence suggests that the oral microbiome has a significant role in triggering atherosclerosis. The present study assessed the oral microbiome composition variation between coronary patients and healthy subjects in order to identify a potential pathogenic signature associated with CAD. We performed metagenomic profiling of salivary microbiomes by 16S ribosomal RNA (rRNA) next-generation sequencing. Oral microbiota profiling was performed for 30 individuals including 20 patients with CAD and ten healthy individuals without carotid plaques or previous stroke or myocardial infarction. We found that oral microbial communities in patients and healthy controls are represented by similar global core oral microbiome. The predominant taxa belonged to Firmicutes (genus Streptococcus, Veillonella, Granulicatella, Selenomonas), Proteobacteria (genus Neisseria, Haemophi...
The WRKY transcription factors superfamily are involved in diverse biological processes in plants... more The WRKY transcription factors superfamily are involved in diverse biological processes in plants including response to biotic and abiotic stresses and plant immunity. Protein-protein interaction network is a useful approach for understanding these complex processes. The availability of Arabidopsis Thaliana interactome offers a good opportunity to do get a global view of protein network. In this work, we have constructed the WRKY transcription factor network by combining different sources of evidence and we characterized its topological features using computational tools. We found that WRKY network is a hub-based network involving multifunctional proteins denoted as hubs such as WRKY 70, WRKY40, WRKY 53, WRKY 60, WRKY 33 and WRKY 51. Functional annotation showed seven functional modules particularly involved in biotic stress and defense responses. Furthermore, the gene ontology and pathway enrichment analysis revealed that WRKY proteins are mainly involved in plant-pathogen interact...
Results regarding the origin and domestication steps of almond and its dissemination around the M... more Results regarding the origin and domestication steps of almond and its dissemination around the Mediterranean basin are very controversial. The general belief is that the domestication was in the eastern side and then its dissemination to the western part was through the different trade routes. A recent study has proved using a combination of nuclear and chloroplast microsatellites a westward dispersal of almond and a long-standing presence of domesticated almond in northern Africa. In order to contribute to this discussion, new interpretation of the previous study using 10 SSRs to analyse 82 almond accessions from different origins was undertaken. The dendogram based on the similarity matrix presented four main clusters. In group A were present the majority of the local genotypes that originate from the centre and the south. Contrarily, all cultivars from the north were in group C and clustered with the European and American genotypes. In fact, the Bayesian-based analysis endorses ...
Olive tree (Olea europaea L.) is mainly grown in the Mediterranean area, which is the most import... more Olive tree (Olea europaea L.) is mainly grown in the Mediterranean area, which is the most important oil-producing crop. In spite of its cultural, economic and nutritional importance, numerous DNA markers accomplished to compositional analyzes by bioinformatic tools have been used to illustrate and reveal homonyms, synonyms and unknown accessions. The objectives of this study were (1) to analyze 5 SNP and 8 SSR markers to characterize 12 olive genotypes originating from different regions of Tunisia and (2) to resolve the denomination ambiguity of Zalmati and Chemlali Tataouine cultivars. Analyses indicated the presence of two erroneous denominations of cultivars.
SARS-CoV-2 across Africa The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-... more SARS-CoV-2 across Africa The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been hard to track in African countries, largely because of patchy data. Wilkinson et al . curated viral genomes collected in 2021 from several countries across the continent. Outbreaks during 2020 in each African country were initiated by imported cases, mostly from Europe. As the pandemic developed, case numbers in African countries were likely many times higher than reported, and subsequent waves of the pandemic appear to have been more severe. Consequently, high-transmission variants have emerged that have spread within the continent, and African countries must be included in global control efforts. —CA
B7-H6 and PD-L1 belong to the B7 family co-stimulatory molecules fine-tuning the immune response.... more B7-H6 and PD-L1 belong to the B7 family co-stimulatory molecules fine-tuning the immune response. The present work investigates the clinical effect of B7-H6 protein expression with PD-L1 status and the infiltration of natural killer cells as potential biomarkers in breast tumor inflammatory microenvironment. The expression levels of B7-H6 protein by cancer cells and immune infiltrating cells in human breast cancer tissues and evaluate their associations with PD-L1 expression, NK cell status, clinical pathological features and prognosis were explored. The immunohistochemistry labeling method was used to assess B7-H6 and PD-L1 proteins expression by cancer and immune cells. The associations between immune checkpoint, major clinical pathological variables and survival rates were analyzed. B7-H6 protein was depicted in both breast and immune cells. Results showed that Tumor B7-H6 expression is highly associated with Her-2 over expression. B7-H6 + immune cells are highly related to the S...
This is the first work performed in the shellfish production area located along the Sfax coasts (... more This is the first work performed in the shellfish production area located along the Sfax coasts (southern Tunisia) on the spatial and temporal patterns of toxic phytoplankton. It relates the excessive introduction of phosphorus in coastal waters from sediments contaminated with that nutrient. A multivariate approach was applyed using data derived from the National Phytoplankton Monitoring Program (REPHY) (2006-2009). We also examine if there is a direct relationship between the abundance of toxic phytoplankton and physical and chemical parameters. This study is based on phytoplankton composition and abundance, as well as physical and chemical data to evaluate the ecological status of the Sfax coasts, at shellfish farms. A total of 13 taxa included in the Intergovernmental Oceanographic Commission (IOC) toxic algae checklist and well-known bloom formers were identified in REPHY. Higher nutrient spring samples were distinguished from those of lower nutrient summer waters. The Redundan...
Auxin is a major regulator of plant growth and development; its action involves transcriptional a... more Auxin is a major regulator of plant growth and development; its action involves transcriptional activation. The identification of Auxin-response element (AuxRE) is one of the most important issues to understand the Auxin regulation of gene expression. Over the past few years, a large number of motif identification tools have been developed. Despite these considerable efforts provided by computational biologists, building reliable models to predict regulatory elements has still been a difficult challenge. In this context, we propose in this work a data fusion approach for the prediction of AuxRE. Our method is based on the combined use of Dempster-Shafer evidence theory and fuzzy theory. To evaluate our model, we have scanning the DORNRÖSCHEN promoter by our model. All proven AuxRE present in the promoter has been detected. At the 0.9 threshold we have no false positive. The comparison of the results of our model and some previous motifs finding tools shows that our model can predict...
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Papers by Ahmed Rebai