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4. Identification of novel proteomic biomarkers for hypertension: a targeted approach for precision medicine.

Author

Aldisi, Rana S., Alsamman, Alsamman M., Krawitz, Peter, Maj, Carlo, and Zayed, Hatem

Subjects
*CORONARY artery disease, *APOLIPOPROTEIN E, *CYTOLOGY, *LIFE sciences, *TWO-way analysis of variance
Abstract

Background: Hypertension is a critical public health issue worldwide. The identification of specific proteomic biomarkers in the Qatari population aims to advance personalized treatment strategies. Methods: We conducted proteomic profiling on 778 Qatari individuals using an aptamer-based SOMAscan platform to analyze 1,305 biomarkers. Statistical analysis involved two-way ANOVA and association analyses with FDR correction, alongside pathway and gene-set enrichment analyses using Reactome and DisGeNET databases. Results: The study identified 26 significant protein biomarkers associated with hypertension. Notably, QORL1 and BMP1 were identified as novel protein biomarkers. Enrichment analysis linked these biomarkers to critical pathways involved in vascular biology, immune system responses, and pathologies like arteriosclerosis and coronary artery disease. Correlation analyses highlighted robust interactions, particularly between QORL1 and various Apolipoprotein E isoforms, suggesting these biomarkers play pivotal roles in the molecular mechanisms underlying hypertension. Conclusions: This research enhances our understanding of the molecular basis of hypertension in the Qatari population and supports the development of precision medicine approaches for treatment. [ABSTRACT FROM AUTHOR]

Published
2025
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5. Assessment of genetic structure and trait associations of Watkins wheat landraces under Egyptian field conditions.

Author

Elkot, Ahmed Fawzy, Nassar, Ahmed E., Elmassry, Elsayed L., Forner-Martínez, Macarena, Awal, Rajani, Wingen, Luzie U., Griffiths, Simon, Alsamman, Alsamman M., and Kehel, Zakaria

Subjects
POPULATION differentiation, PRINCIPAL components analysis, WHEAT breeding, GENOME-wide association studies, PLANT chromosomes
Abstract

Background: Wheat landraces represent a reservoir of genetic diversity that can support wheat improvement through breeding. A core panel of 300 Watkins wheat landraces, as well as 16 non-Watkins landraces and elite wheat cultivars, was grown during the 2020–2021 and 2021–2022 seasons at four Agricultural Research Stations in Egypt, Gemmiza, Nubaria, Sakha, and Sids, to evaluate the core panel for agromorphological and yield-related traits. The genetic population structure within these genotypes were assessed using 35,143 single nucleotide polymorphisms (SNPs). Results: Cluster analyses using Discriminant Analysis of Principal Components (DAPC) and k-means revealed three clusters with moderate genetic differentiation and population structure, possibly due to wheat breeding systems and geographical isolation. The best ancestry was k = 4, but k = 2 and k = 3 were also significant. A genome-wide association study (GWAS) identified clustered marker trait associations (MTAs) linked to thousand kernel weight on chromosome 5A, plant height on chromosomes 3B and 1D, days to heading on chromosomes 2A, 4B, 5B and 1D, and plant maturity on chromosomes 3A, 2B, and 6B. In the future, these MTAs can be used to accelerate the incorporation of beneficial alleles into locally adapted germplasm through marker-assisted selection. Gene enrichment analysis identified key genes within these loci, including Reduced height-1 (Rht-A1) and stress-related genes. Conclusion: These findings underscore significant genetic connections and the involvement of crucial biological pathways. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Transcriptomic insights into mycorrhizal interactions with tomato root: a comparative study of short- and long-term post-inoculation responses.

Author

Abdelsattar, Mohamed, Soliman, Maali S., Mohamed, Rasha A., Radwan, Khaled H., El-Mahdy, Mohamed M., Mousa, Khaled H., Khalil, Shaimaa R. M., Osman, Engy, Alameldin, Hussien F., Hussein, Ahmed, Hassanein, Sameh E., Abdallah, Naglaa A., Alsamman, Alsamman M., and Osama, Omnia

Subjects
ION transport (Biology), PLANT genes, TOMATOES, CELL division, PHYTOPATHOGENIC fungi
Abstract

Background: Arbuscular mycorrhiza (AM) refers to a symbiotic association between plant roots and fungi that enhances the uptake of mineral nutrients from the soil and enables the plant to tolerate abiotic and biotic stresses. Although previously reported RNA-seq analyses have identified large numbers of AM-responsive genes in model plants, such as Solanum lycopersicum L., further studies are underway to comprehensively understand the complex interactions between plant roots and AM, especially in terms of the short- and long-term responses after inoculation. Results: Herein, we used RNA-seq technology to obtain the transcriptomes of tomato roots inoculated with the fungus Rhizophagus irregularis at 7 and 30 days post inoculation (dpi). Of the 1,019 differentially expressed genes (DEGs) in tomato roots, 635 genes showed differential expressions between mycorrhizal and non-mycorrhizal associations at the two time points. The number of upregulated DEGs far exceeded the number of downregulated ones at 7 dpi, and this difference decreased at 30 dpi. Several notable genes were particularly involved in the plant defense, plant growth and development, ion transport, and biological processes, namely, GABAT, AGP, POD, NQO1, MT4, MTA, and AROGP3. In addition, the Kyoto encyclopedia of genes and genomes pathway enrichment analysis revealed that some of the genes were involved in different pathways, including those of ascorbic acid (AFRR, GME1, and APX), metabolism (CYP, GAPC2, and CAM2), and sterols (CYC1 and HMGR), as well as genes related to cell division and cell cycle (CDKB2 and PCNA). Conclusion: These findings provide valuable new data on AM-responsive genes in tomato roots at both short- and long-term postinoculation stages, enabling the deciphering of biological interactions between tomato roots and symbiotic fungi. [ABSTRACT FROM AUTHOR]

Published
2024
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17. Evolving strategies and application of proteins and peptide therapeutics in cancer treatment

Author

Mukherjee, Anirban Goutam, primary, Wanjari, Uddesh Ramesh, additional, Gopalakrishnan, Abilash Valsala, additional, Bradu, Pragya, additional, Biswas, Antara, additional, Ganesan, Raja, additional, Renu, Kaviyarasi, additional, Dey, Abhijit, additional, Vellingiri, Balachandar, additional, El Allali, Achraf, additional, Alsamman, Alsamman M., additional, Zayed, Hatem, additional, and George Priya Doss, C., additional

Published
2023
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18. Identification, characterization, and validation of NBS-encoding genes in grass pea

Author

Alsamman, Alsamman M., primary, Mousa, Khaled H., additional, Nassar, Ahmed E., additional, Faheem, Mostafa M., additional, Radwan, Khaled H., additional, Adly, Monica H., additional, Hussein, Ahmed, additional, Istanbuli, Tawffiq, additional, Mokhtar, Morad M., additional, Elakkad, Tamer Ahmed, additional, Kehel, Zakaria, additional, Hamwieh, Aladdin, additional, Abdelsattar, Mohamed, additional, and El Allali, Achraf, additional

Published
2023
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21. Genome-wide identification, characterization, and validation of the bHLH transcription factors in grass pea

Author

Alsamman, Alsamman M., primary, Abdelsattar, Mohamed, additional, El Allali, Achraf, additional, Radwan, Khaled H., additional, Nassar, Ahmed E., additional, Mousa, Khaled H., additional, Hussein, Ahmed, additional, Mokhtar, Morad M., additional, Abd El-Maksoud, Mamdouh M., additional, Istanbuli, Tawffiq, additional, Kehel, Zakaria, additional, and Hamwieh, Aladdin, additional

Published
2023
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22. Two major chromosome evolution events with unrivaled conserved gene content in pomegranate

Author

Akparov, Zeynal, primary, Hajiyeva, Sabina, additional, Abbasov, Mehraj, additional, Kaur, Sukhjiwan, additional, Hamwieh, Aladdin, additional, Alsamman, Alsamman M., additional, Hajiyev, Elchin, additional, Babayeva, Sevda, additional, Izzatullayeva, Vusala, additional, Mustafayeva, Ziyafat, additional, Mehdiyeva, Sabina, additional, Mustafayev, Orkhan, additional, Shahmuradov, Ilham, additional, Kosarev, Peter, additional, Solovyev, Victor, additional, Salamov, Asaf, additional, and Jighly, Abdulqader, additional

Published
2023
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24. The Implication of Mechanistic Approaches and the Role of the Microbiome in Polycystic Ovary Syndrome (PCOS): A Review

Author

Mukherjee, Anirban Goutam, primary, Wanjari, Uddesh Ramesh, additional, Kannampuzha, Sandra, additional, Murali, Reshma, additional, Namachivayam, Arunraj, additional, Ganesan, Raja, additional, Dey, Abhijit, additional, Babu, Achsha, additional, Renu, Kaviyarasi, additional, Vellingiri, Balachandar, additional, Ramanathan, Gnanasambandan, additional, Priya Doss C., George, additional, Elsherbiny, Nehal, additional, Elsherbini, Amira M., additional, Alsamman, Alsamman M., additional, Zayed, Hatem, additional, and Gopalakrishnan, Abilash Valsala, additional

Published
2023
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28. Genetic Dissection of Heat Stress Tolerance in Faba Bean (Vicia faba L.) Using GWAS

Author

Maalouf, Fouad, Abou-Khater, Lynn, Babiker, Zayed, Jighly, Abdulqader, Alsamman, Alsamman M., Hu, Jinguo, Ma, Yu, Rispail, Nicolas, Balech, Rind, Hamweih, Aladdin, Baum, Michael, Kumar, Shiv, Maalouf, Fouad, Abou-Khater, Lynn, Babiker, Zayed, Jighly, Abdulqader, Alsamman, Alsamman M., Hu, Jinguo, Ma, Yu, Rispail, Nicolas, Balech, Rind, Hamweih, Aladdin, Baum, Michael, and Kumar, Shiv

Abstract

Heat waves are expected to become more frequent and intense, which will impact faba bean cultivation globally. Conventional breeding methods are effective but take considerable time to achieve breeding goals, and, therefore, the identification of molecular markers associated with key genes controlling heat tolerance can facilitate and accelerate efficient variety development. We phenotyped 134 accessions in six open field experiments during summer seasons at Terbol, Lebanon, at Hudeiba, Sudan, and at Central Ferry, WA, USA from 2015 to 2018. These accessions were genotyped using genotyping by sequencing (GBS), and 10,794 high quality single nucleotide polymorphisms (SNPs) were discovered. These accessions were clustered in one diverse large group, although several discrete groups may exist surrounding it. Fifteen lines belonging to different botanical groups were identified as tolerant to heat. SNPs associated with heat tolerance using single-trait (ST) and multi-trait (MT) genome-wide association studies (GWASs) showed 9 and 11 significant associations, respectively. Through the annotation of the discovered significant SNPs, we found that SNPs from transcription factor helix–loop–helix bHLH143-like S-adenosylmethionine carrier, putative pentatricopeptide repeat-containing protein At5g08310, protein NLP8-like, and photosystem II reaction center PSB28 proteins are associated with heat tolerance.

Published
2022

29. Genomic regions associated with herbicide tolerance in a worldwide faba bean (Vicia faba L.) collection [Dataset]

Author

Abou-Khater, Lynn, Maalouf, Fouad, Jighly, Abdulqader, Alsamman, Alsamman M., Rubiales, Diego, Rispail, Nicolas, Hu, Jinguo, Ma, Yu, Balech, Rind, Hamwieh, Aladdin, Baum, Michael, Kumar, Shiv, Abou-Khater, Lynn, Maalouf, Fouad, Jighly, Abdulqader, Alsamman, Alsamman M., Rubiales, Diego, Rispail, Nicolas, Hu, Jinguo, Ma, Yu, Balech, Rind, Hamwieh, Aladdin, Baum, Michael, and Kumar, Shiv

Abstract

Supplementary Table S1. SNP-trait associations revealed by the ST-GWAS analysis. Underscored SNPs represents the highly significant associations, while SNPs in italic represents the SNPs associated with multiple traits. Supplementary Table S2. Gene annotation information of some of the highly significant NPSs-traits associations. Supplementary Table S3. Details of the traits recorded at each experiment; traits are coded as the environment, followed by the trait, the treatment and “RI” if the number describe a reduction index. Supplementary Table S4. Description of the damages observed in the treated plants for each herbicide damage score (HDS).

Published
2022

30. Genetic Dissection of Heat Stress Tolerance in Faba Bean (Vicia faba L.) Using GWAS

Author

Arab Fund for Economic and Social Development, Maalouf, Fouad, Abou-Khater, Lynn, Babiker, Zayed, Jighly, Abdulqader, Alsamman, Alsamman M., Hu, Jinguo, Ma, Yu, Rispail, Nicolas, Balech, Rind, Hamweih, Aladdin, Baum, Michael, Kumar, Shiv, Arab Fund for Economic and Social Development, Maalouf, Fouad, Abou-Khater, Lynn, Babiker, Zayed, Jighly, Abdulqader, Alsamman, Alsamman M., Hu, Jinguo, Ma, Yu, Rispail, Nicolas, Balech, Rind, Hamweih, Aladdin, Baum, Michael, and Kumar, Shiv

Abstract

Heat waves are expected to become more frequent and intense, which will impact faba bean cultivation globally. Conventional breeding methods are effective but take considerable time to achieve breeding goals, and, therefore, the identification of molecular markers associated with key genes controlling heat tolerance can facilitate and accelerate efficient variety development. We phenotyped 134 accessions in six open field experiments during summer seasons at Terbol, Lebanon, at Hudeiba, Sudan, and at Central Ferry, WA, USA from 2015 to 2018. These accessions were genotyped using genotyping by sequencing (GBS), and 10,794 high quality single nucleotide polymorphisms (SNPs) were discovered. These accessions were clustered in one diverse large group, although several discrete groups may exist surrounding it. Fifteen lines belonging to different botanical groups were identified as tolerant to heat. SNPs associated with heat tolerance using single-trait (ST) and multi-trait (MT) genome-wide association studies (GWASs) showed 9 and 11 significant associations, respectively. Through the annotation of the discovered significant SNPs, we found that SNPs from transcription factor helix-loop-helix bHLH143-like S-adenosylmethionine carrier, putative pentatricopeptide repeat-containing protein At5g08310, protein NLP8-like, and photosystem II reaction center PSB28 proteins are associated with heat tolerance.

Published
2022

31. Genomic regions associated with herbicide tolerance in a worldwide faba bean (Vicia faba L.) collection

Author

Arab Fund for Economic and Social Development, Abou-Khater, Lynn, Maalouf, Fouad, Jighly, Abdulqader, Alsamman, Alsamman M., Rubiales, Diego, Rispail, Nicolas, Hu, Jinguo, Ma, Yu, Balech, Rind, Hamwieh, Aladdin, Baum, Michael, Kumar, Shiv, Arab Fund for Economic and Social Development, Abou-Khater, Lynn, Maalouf, Fouad, Jighly, Abdulqader, Alsamman, Alsamman M., Rubiales, Diego, Rispail, Nicolas, Hu, Jinguo, Ma, Yu, Balech, Rind, Hamwieh, Aladdin, Baum, Michael, and Kumar, Shiv

Abstract

Weeds represent one of the major constraints for faba bean crop. The identification of molecular markers associated with key genes imparting tolerance to herbicides can facilitate and fasten the efficient and effective development of herbicide tolerant cultivars. We phenotyped 140 faba bean genotypes in three open field experiments at two locations in Lebanon and Morocco against three herbicide treatments (T1 metribuzin 250 g ai/ha; T2 imazethapyr 75 g ai/ha; T3 untreated) and one in greenhouse where T1 and T3 were applied. The same set was genotyped using genotyping by sequencing (GBS) which yield 10,794 high quality single nucleotide polymorphisms (SNPs). ADMIXTURE software was used to infer the population structure which revealed two ancestral subpopulations. To identify SNPs associated with phenological and yield related traits under herbicide treatments, Single-trait (ST) and Multi-trait (MT) Genome Wide Association Studies (GWAS) were fitted using GEMMA software, showing 10 and 14 highly significant associations, respectively. Genomic sequences containing herbicide tolerance associated SNPs were aligned against the NCBI database using BLASTX tool using default parameters to annotate candidate genes underlying the causal variants. SNPs from acidic endochitinase, LRR receptor-like serine/threonine-protein kinase RCH1, probable serine/threonine-protein kinase NAK, malate dehydrogenase, photosystem I core protein PsaA and MYB-related protein P-like were significantly associated with herbicide tolerance traits.

Published
2022

33. Novel Genomic Regions Linked to Ascochyta Blight Resistance in Two Differentially Resistant Cultivars of Chickpea

Author

Alo, Fida, primary, Rani, Anupalli Roja, additional, Baum, Michael, additional, Singh, Sarvjeet, additional, Kehel, Zakaria, additional, Rani, Upasana, additional, Udupa, Sripada, additional, Al-Sham’aa, Khaled, additional, Alsamman, Alsamman M., additional, Istanbuli, Tawffiq, additional, Attar, Basem, additional, Hamwieh, Aladdin, additional, and Amri, Ahmed, additional

Published
2022
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